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Singh S, Choudhary M. Unusual Ni⋯Ni interaction in Ni(ii) complexes as potential inhibitors for the development of new anti-SARS-CoV-2 Omicron drugs. RSC Med Chem 2024; 15:895-915. [PMID: 38516589 PMCID: PMC10953495 DOI: 10.1039/d3md00601h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/05/2024] [Indexed: 03/23/2024] Open
Abstract
Two nickel(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) of a tetradentate Schiff base ligand (H2L) derived from 2-hydroxy-1-naphthaldehyde with ethylenediamine were synthesized, designed, and characterized via spectroscopic and single crystal XRD analyses. Both nickel(ii) complexes exhibited unusual Ni⋯Ni interactions and were fully characterized via single-crystal X-ray crystallography. Nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) crystallize in monoclinic and triclinic crystal systems with P21/c and P1̄ space groups, respectively, and revealed square planar geometry around each Ni(ii) ion. The structure of both the complexes have established the existence of a new kind of metal system containing nickel(ii)-nickel(ii) interactions with a square planar-like geometry about the nickel(ii) atoms. Both square planar Ni(ii) complexes were often stacked with relatively short Ni⋯Ni distances. The non-bonded Ni-Ni distance (Ni⋯Ni separation) seems to be 3.356 Å and 3.214 Å from the nickel atoms of [Ni(L)]2(1) and [Ni(L)]n(2), respectively. These distances are shorter than the sum of their van der Waals radii (4.80 Å) but longer than the sum of their covalent radii (2.50 Å), indicating that there is a Ni⋯Ni interaction but not a Ni-Ni bond. The discrete molecules are π-stacked and connected via weak intermolecular interactions (C-H⋯O and C-H⋯N). Cyclic voltammetry measurements were obtained for both the complexes, and their pharmacokinetic and chemoinformatics properties were also explored. Detailed structural analysis and non-covalent supramolecular interactions were investigated using single-crystal structure analysis and computational approaches. Both the unique structures show good inhibition performance for the Omicron spike proteins of the SARS CoV-2 virus. To gain insights into potential SARS-CoV-2 Omicron drugs and find inhibitors against the Omicron variants of SARS-CoV-2, we examined the molecular docking of the nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron spike protein (PDB ID: 7WK2 and 7WVO). A strong binding was predicted between Ni(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron variant receptor protein through the negative value of binding affinity. Molecular docking of Nil(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with a DNA duplex (PDB ID: 7D3T) and RNA (PDB ID: 7TDC) binding protein was also studied. Overall, this study suggests that Ni(ii) complexes can be considered as drug candidates against the Omicron variants of SARS-CoV-2.
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Affiliation(s)
- Simranjeet Singh
- Department of Chemistry, National Institute of Technology Patna Patna-800005 Bihar India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna Patna-800005 Bihar India
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2
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Knight IS, Mailhot O, Tang KG, Irwin JJ. DockOpt: A Tool for Automatic Optimization of Docking Models. J Chem Inf Model 2024; 64:1004-1016. [PMID: 38206771 PMCID: PMC10865354 DOI: 10.1021/acs.jcim.3c01406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024]
Abstract
Molecular docking is a widely used technique for leveraging protein structure for ligand discovery, but it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress toward automation, docking still requires expert guidance, hindering its adoption by a broader range of investigators. To make docking more accessible, we developed a new utility called DockOpt, which automates the creation, evaluation, and optimization of docking models prior to their deployment in large-scale prospective screens. DockOpt outperforms our previous automated pipeline across all 43 targets in the DUDE-Z benchmark data set, and the generated models for 84% of targets demonstrate sufficient enrichment to warrant their use in prospective screens, with normalized LogAUC values of at least 15%. DockOpt is available as part of the Python package Pydock3 included in the UCSF DOCK 3.8 distribution, which is available for free to academic researchers at https://dock.compbio.ucsf.edu and free for everyone upon registration at https://tldr.docking.org.
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Affiliation(s)
- Ian S. Knight
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - Olivier Mailhot
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - Khanh G. Tang
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
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3
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Navarrete E, Morales P, Muñoz-Osses M, Vásquez-Martínez Y, Godoy F, Maldonado T, Martí AA, Flores E, Mascayano C. Evaluating the inhibitory activity of ferrocenyl Schiff bases derivatives on 5-lipoxygenase: Computational and biological studies. J Inorg Biochem 2023; 245:112233. [PMID: 37141763 DOI: 10.1016/j.jinorgbio.2023.112233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/05/2023] [Accepted: 04/15/2023] [Indexed: 05/06/2023]
Abstract
In the search for new 5-LOX inhibitors, two ferrocenyl Schiff base complexes functionalized with catechol ((ƞ5-(E)-C5H4-NCH-3,4-benzodiol)Fe(ƞ5-C5H5) (3a)) and vanillin ((ƞ5-(E)-C5H4-NCH-3-methoxy-4-phenol)Fe(ƞ5-C5H5) (3b)) were obtained. Complexes 3a and 3b were biologically evaluated as 5-LOX inhibitors showed potent inhibition compared to their organic analogs (2a and 2b) and known commercial inhibitors, with IC50 = 0.17 ± 0.05 μM for (3a) and 0.73 ± 0.06 μM for (3b) demonstrated a highly inhibitory and potent effect against 5-LOX due to the incorporation of the ferrocenyl fragment. Molecular dynamic studies showed a preferential orientation of the ferrocenyl fragment toward the non-heme iron of 5-LOX, which, together with electrochemical and in-vitro studies, allowed us to propose a competitive redox deactivation mechanism mediated by water, where Fe(III)-enzyme can be reduced by the ferrocenyl fragment. An Epa/IC50 relationship was observed, and the stability of the Schiff bases was evaluated by SWV in the biological medium, observing that the hydrolysis does not affect the high potency of the complexes, making them interesting alternatives for pharmacological applications.
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Affiliation(s)
| | - Pilar Morales
- Departamento Ciencias del Ambiente, Universidad de Santiago de Chile, Chile
| | | | - Yesseny Vásquez-Martínez
- Programa Centro de Investigaciones Biomédicas y Aplicadas (CIBAP), Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Chile
| | - Fernando Godoy
- Departamento Química de los Materiales, Universidad de Santiago de Chile, Chile
| | - Tamara Maldonado
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Casilla 4059, Valparaíso, Chile
| | - Angel A Martí
- Department of Chemistry, Bioengineering and Materials Science & Nanoengineering, Rice University, Houston, TX 77005, United States
| | - Erick Flores
- Departamento Química de los Materiales, Universidad de Santiago de Chile, Chile.
| | - Carolina Mascayano
- Departamento Ciencias del Ambiente, Universidad de Santiago de Chile, Chile.
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Kumar S, Choudhary M. Design and molecular docking studies of {N 1-[2-(amino)ethyl]ethane-1,2-diamine}-[tris(oxido)]-molybdenum(VI) complex as a potential antivirus drug: from synthesis to structure. J COORD CHEM 2023. [DOI: 10.1080/00958972.2023.2173589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
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Aprajita, Choudhary M. New Ni(II) and Cu(II) Schiff base coordination complexes derived from 5-Bromo-salicylaldehyde and 3-picoyl amine/ethylenediamine: Synthesis, structure, Hirshfeld surface and molecular docking study with SARS-CoV-2 7EFP-main protease. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kumar S, Choudhary M. New nickel( ii) Schiff base complexes as potential tools against SARS-CoV-2 Omicron target proteins: an in silico approach. NEW J CHEM 2023. [DOI: 10.1039/d2nj05136b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, we report the in silico design and synthesis of two new nickel(ii) coordination complexes, based on Schiff bases derived from the 2-hydroxy-1-naphthaldehyde moiety.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
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Zheng SJ, Zheng N, Zhang ML, Wu FF, Yang SD, Cheng XH, Bao HY, Zhang R. Probing the binding mechanism of the verbascoside and human serum albumin by fluorescence spectroscopy and molecular docking approach. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-03002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Aprajita, Choudhary M. Design, synthesis and characterization of novel Ni(II) and Cu(II) complexes as antivirus drug candidates against SARS-CoV-2 and HIV virus. J Mol Struct 2022; 1263:133114. [PMID: 35465175 PMCID: PMC9017811 DOI: 10.1016/j.molstruc.2022.133114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/16/2022] [Indexed: 12/16/2022]
Abstract
This paper describes the structure-based design, synthesis and anti-virus effect of two new coordination complexes, a Ni(II) complex [Ni(L)2] (1) and a Cu(II) complex [Cu(L)2] (2) of (E)-N-phenyl-2-(thiophen-2-ylmethylene) hydrazine-1-carbothioamide(HL). The synthesized ligand was coordinated to metal ions through the bidentate-N, S donor atoms. The newly synthesized complexes were characterized by various spectroscopic and physiochemical methods, powdered XRD analysis and also X-ray crystallography study. Ni(II) complex [Ni(L)2](1) crystallize in orthorhombic crystal system with the space group Pbca with four molecules in the unit cell (a = 9.857(3) Å, b = 7.749(2) Å, c = 32.292(10) Å, α = 90°, β = 90°, γ = 90°, Z= 4) and reveals a distorted square planar geometry. A Hirshfeld surface and 2D fingerprint plot has been explored in the crystal structure of Ni(II) complex [Ni(L)2] (1). Energy framework computational analysia has also been explored. DFT based calculations have been performed on the Schiff base and its metal complexes to study the structure-property relationship. Furthermore, the molecular docking studies of the ligand and its metal complexes with SARS-CoV-2 virus (PDB ID: 7BZ5) and HIV-1 virus (PDB ID: 6MQA) are also investigated. The molecular docking calculations of the Ni(II) complex [Ni(L)2] (1) and a Cu(II) complex [Cu(L)2] (2) with SARS-CoV-2 virus revealed that the binding affinities at inhibition binding site of receptor protein are 9.7 kcal/mol and -9.3 kcal/mol, respectively. The molecular docking results showed that the binding affinities of Ni(II) complex (1) and Cu(II) complex (2) against SARS-CoV-2 virus were found comparatively higher than the HIV-1 virus (-8.5 kcal/mol and -8.2 kcal/mol, respectively). As potential drug candidates, Swiss-ADME predictions analyses are also studied and the results are compared with Chloroquine (CQ) and Hydroxychloroquine (HCQ) as anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Aprajita
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar 800005, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar 800005, India
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Deepika G, Subbarayadu S, Chaudhary A, Sarma PVGK. Dibenzyl (benzo [d] thiazol-2-yl (hydroxy) methyl) phosphonate (DBTMP) showing anti-S. aureus and anti-biofilm properties by elevating activities of serine protease (SspA) and cysteine protease staphopain B (SspB). Arch Microbiol 2022; 204:397. [PMID: 35708833 DOI: 10.1007/s00203-022-02974-y] [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: 11/16/2021] [Revised: 04/26/2022] [Accepted: 05/11/2022] [Indexed: 11/02/2022]
Abstract
Staphylococcus aureus biofilms are the pathogenic factor in the spread of infection and are more pronounced in multidrug-resistant strains of S. aureus, where high expression of proteases is observed. Among various proteases, Serine protease (SspA) and cysteine protease Staphopain B (SspB) are known to play a key role in the biofilm formation and removal of biofilms. In earlier studies, we have reported Dibenzyl (benzo [d] thiazol-2-yl (hydroxy) methyl) phosphonate (DBTMP) exhibits anti-S. aureus and anti-biofilm properties by elevating the expression of the protease. In this study, the effect of DBTMP on the activities of SspA, and SspB of S. aureus was evaluated. The SspA and SspB genes of S. aureus ATCC12600 were sequenced (Genbank accession numbers: MZ456982 and MW574006). In S. aureus active SspA is formed by proteolytic cleavage of immature SspA, to get this mature SspA (mSspA), we have PCR amplified the mSspA sequence from the SspA gene. The mSspA and SspB genes were cloned, expressed, and characterized. The pure recombinant proteins rSspB and rmSspA exhibited a single band in SDS-PAGE with a molecular weight of 40 and 30 KD, respectively. The activities of rmSspA and rSspB are 32.33 and 35.45 Units/mL correspondingly. DBTMP elevated the activities of rmSspA and rSspB by docking with respective enzymes. This compound disrupted the biofilms formed by the multidrug-resistant strains of S. aureus and further prevented biofilm formation. These findings explain that DBTMP possesses anti-S. aureus and anti-biofilm features.
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Affiliation(s)
- G Deepika
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, 517507, India
| | - S Subbarayadu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, 517507, India
| | - Abhijit Chaudhary
- Department of Microbiology, Sri Padmavati Medical College (Women), SVIMS, Tirupati, Andhra Pradesh, 517507, India
| | - P V G K Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, 517507, India.
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Ilic VK, Egorova O, Tsang E, Gatto M, Wen Y, Zhao Y, Sheng Y. Hinokiflavone Inhibits MDM2 Activity by Targeting the MDM2-MDMX RING Domain. Biomolecules 2022; 12:biom12050643. [PMID: 35625571 PMCID: PMC9138535 DOI: 10.3390/biom12050643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/17/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
The proto-oncogene MDM2 is frequently amplified in many human cancers and its overexpression is clinically associated with a poor prognosis. The oncogenic activity of MDM2 is demonstrated by its negative regulation of tumor suppressor p53 and the substrate proteins involved in DNA repair, cell cycle control, and apoptosis pathways. Thus, inhibition of MDM2 activity has been pursued as an attractive direction for the development of anti-cancer therapeutics. Virtual screening was performed using the crystal structure of the MDM2-MDMX RING domain dimer against a natural product library and identified a biflavonoid Hinokiflavone as a promising candidate compound targeting MDM2. Hinokiflavone was shown to bind the MDM2-MDMX RING domain and inhibit MDM2-mediated ubiquitination in vitro. Hinokiflavone treatment resulted in the downregulation of MDM2 and MDMX and induction of apoptosis in various cancer cell lines. Hinokiflavone demonstrated p53-dependent and -independent tumor-suppressive activity. This report provides biochemical and cellular evidence demonstrating the anti-cancer effects of Hinokiflavone through targeting the MDM2-MDMX RING domain.
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Affiliation(s)
- Viktoria K. Ilic
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada; (V.K.I.); (O.E.); (E.T.); (M.G.); (Y.W.)
| | - Olga Egorova
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada; (V.K.I.); (O.E.); (E.T.); (M.G.); (Y.W.)
| | - Ernest Tsang
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada; (V.K.I.); (O.E.); (E.T.); (M.G.); (Y.W.)
| | - Milena Gatto
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada; (V.K.I.); (O.E.); (E.T.); (M.G.); (Y.W.)
| | - Yi Wen
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada; (V.K.I.); (O.E.); (E.T.); (M.G.); (Y.W.)
| | - Yong Zhao
- Beijing Computing Center, Beijing Academy of Science and Technology, Beijing, 100094, China;
| | - Yi Sheng
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada; (V.K.I.); (O.E.); (E.T.); (M.G.); (Y.W.)
- Correspondence: ; Tel.: 1-416-7362100 (ext. 33521)
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Shanak S, Bassalat N, Barghash A, Kadan S, Ardah M, Zaid H. Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:2832889. [PMID: 35356248 PMCID: PMC8958086 DOI: 10.1155/2022/2832889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/16/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
The growing smooth talk in the field of natural compounds is due to the ancient and current interest in herbal medicine and their potentially positive effects on health. Dozens of antidiabetic natural compounds were reported and tested in vivo, in silico, and in vitro. The role of these natural compounds, their actions on the insulin signaling pathway, and the stimulation of the glucose transporter-4 (GLUT4) insulin-responsive translocation to the plasma membrane (PM) are all crucial in the treatment of diabetes and insulin resistance. In this review, we collected and summarized a group of available in vivo and in vitro studies which targeted isolated phytochemicals with possible antidiabetic activity. Moreover, the in silico docking of natural compounds with some of the insulin signaling cascade key proteins is also summarized based on the current literature. In this review, hundreds of recent studies on pure natural compounds that alleviate type II diabetes mellitus (type II DM) were revised. We focused on natural compounds that could potentially regulate blood glucose and stimulate GLUT4 translocation through the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. On attempt to point out potential new natural antidiabetic compounds, this review also focuses on natural ingredients that were shown to interact with proteins in the insulin signaling pathway in silico, regardless of their in vitro/in vivo antidiabetic activity. We invite interested researchers to test these compounds as potential novel type II DM drugs and explore their therapeutic mechanisms.
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Affiliation(s)
- Siba Shanak
- Faculty of Sciences, Arab American University, P.O Box 240, Jenin, State of Palestine
| | - Najlaa Bassalat
- Faculty of Sciences, Arab American University, P.O Box 240, Jenin, State of Palestine
- Faculty of Medicine, Arab American University, P.O Box 240, Jenin, State of Palestine
| | - Ahmad Barghash
- Computer Science Department, German Jordanian University, Madaba Street. P.O. Box 35247, Amman 11180, Jordan
| | - Sleman Kadan
- Qasemi Research Center, Al-Qasemi Academic College, P.O Box 124, Baqa El-Gharbia 30100, Israel
| | - Mahmoud Ardah
- Faculty of Sciences, Arab American University, P.O Box 240, Jenin, State of Palestine
| | - Hilal Zaid
- Faculty of Medicine, Arab American University, P.O Box 240, Jenin, State of Palestine
- Qasemi Research Center, Al-Qasemi Academic College, P.O Box 124, Baqa El-Gharbia 30100, Israel
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12
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Zhao Y, Tian Y, Pan C, Liang A, Zhang W, Sheng Y. Target-Based In Silico Screening for Phytoactive Compounds Targeting SARS-CoV-2. Interdiscip Sci 2022; 14:64-79. [PMID: 34308530 PMCID: PMC8310681 DOI: 10.1007/s12539-021-00461-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 12/18/2022]
Abstract
Coronavirus disease 2019 (COVID-19), resulting from infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can cause severe and fatal pneumonia along with other life-threatening complications. The COVID-19 pandemic has taken a heavy toll on the healthcare system globally and has hit the economy hard in all affected countries. As a result, there is an unmet medical need for both the prevention and treatment of COVID-19 infection. Several herbal remedies have claimed to show promising clinical results, but the mechanisms of action are not clear. We set out to identify the anti-viral natural products of these herbal remedies that presumably inhibit the life cycle of SARS-CoV-2. Particularly we chose four key SARS-CoV-2 viral enzymes as targets: Papain-like protease, Main protease, RNA dependent RNA polymerase, and 2'-O-ribose methyltransferase, which were subjected to an unbiased in silico screening against a small molecule library of 33,765 compounds originating from herbs and medicinal plants. The small molecules were then ranked based on their free energy of fitting into the "druggable" pockets on the surface of each target protein. We have analyzed the best "fit" molecules and annotated them according to their plant sources and pharmacokinetic properties. Here we present a list of potential anti-viral ingredients of herbal remedies targeting SARS-CoV-2 and explore the potential mechanisms of action of these compounds as a framework for further development of chemoprophylaxis agents against COVID-19.
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Affiliation(s)
- Yong Zhao
- Beijing Computing Center, Beijing Academy of Science and Technology, 7 Fengxian Road, Beijing, 100094, China.
| | - Yu Tian
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China.
| | - Chenling Pan
- Beijing Computing Center, Beijing Academy of Science and Technology, 7 Fengxian Road, Beijing, 100094, China
| | - Aihua Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wei Zhang
- The Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Yi Sheng
- The Department of Biology, York University, Life Sciences Building 327B, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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Ragunathan V, Chithra K, Shivanika C, Sudharsan MS. Modelling and targeting mitochondrial protein tyrosine phosphatase 1: a computational approach. In Silico Pharmacol 2022; 10:3. [PMID: 35111562 PMCID: PMC8762535 DOI: 10.1007/s40203-022-00119-z] [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: 05/03/2021] [Accepted: 01/03/2022] [Indexed: 01/19/2023] Open
Abstract
The present research scintillates on the homology modelling of rat mitochondrial protein tyrosine phosphatase 1 (PTPMT1) and targeting its activity using flavonoids through a computational docking approach. PTPMT1 is a dual-specificity phosphatase responsible for protein phosphorylation and plays a vital role in the metabolism of cardiolipin biosynthesis, insulin regulation, etc. The inhibition of PTPMT1 has also shown enhanced insulin levels. The three-dimensional structure of the protein is not yet known. The homology modelling was performed using SWISS-MODEL and Geno3D webservers to compare the efficiencies. The PROCHECK for protein modelled using SWISS-MODEL showed 91.6% of amino acids in the most favoured region, 0.7% residues in the disallowed region that was found to be significant compared to the model built using Geno3D. 210 common flavonoids were docked in the modelled protein using the AutoDock 4.2.6 along with a control drug alexidine dihydrochloride. Our results show promising candidates that bind protein tyrosine phosphatase 1, including, prunin (- 8.66 kcal/mol); oroxindin (- 8.56 kcal/mol); luteolin 7-rutinoside (- 8.47 kcal/mol); 3(2H)-isoflavenes (- 8.36 kcal/mol); nicotiflorin (- 8.29 kcal/mol), ranked top in the docking experiments. We predicted the pharmacokinetic and Lipinski properties of the top ten compounds with the lowest binding energies. To further validate the stability of the modelled protein and docked complexes molecular dynamics simulations were performed using Desmond, Schrodinger for 150 ns in conjunction with MM-GBSA. Thus, flavonoids could act as potential inhibitors of PTPMT1, and further, in-vitro and in-vivo studies are essential to complete the drug development process.
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Affiliation(s)
- Venkataraghavan Ragunathan
- grid.252262.30000 0001 0613 6919Nanomaterials and Environmental Research Laboratory, Department of Chemical Engineering, Alagappa College of Technology, Anna University, Chennai, 600025 India
| | - K. Chithra
- grid.252262.30000 0001 0613 6919Nanomaterials and Environmental Research Laboratory, Department of Chemical Engineering, Alagappa College of Technology, Anna University, Chennai, 600025 India
| | - C. Shivanika
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore Campus, Vellore, Tamil Nadu 632014 India
| | - Meenambiga Setti Sudharsan
- grid.412815.b0000 0004 1760 6324Department of Bioengineering, School of Engineering, Vels Institute of Science Technology and Advanced Studies, Pallavaram, Chennai, 600117 India
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14
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Kumar S, Choudhary M. Structure-based design and synthesis of copper( ii) complexes as antivirus drug candidates targeting SARS CoV-2 and HIV. NEW J CHEM 2022. [DOI: 10.1039/d2nj00703g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the structure-based design and synthesis of two novel square-planar trans-N2O2 Cu(ii) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) of 2-((Z)-(4-methoxyphenylimino)methyl)-4,6-dichlorophenol (L1H) and 2-((Z)-(2,4-dibromophenylimino)methyl)-4-bromophenol (L2H) as potential inhibitors against the main protease of the SARS-CoV-2 and HIV viruses.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
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15
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Lim JPL, Braza MKE, Nellas RB. The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor - retinoid X receptor. J Mol Graph Model 2021; 104:107829. [PMID: 33450664 DOI: 10.1016/j.jmgm.2020.107829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022]
Abstract
Ligand-based allostery has been gaining attention for its importance in protein regulation and implication in drug design. One of the interesting cases of protein allostery is the thyroid hormone receptor - retinoid x receptor (TR:RXR), which regulates the gene expression of important physiological processes, such as development and metabolism. It is regulated by the TR native ligand triiodothyronine (T3), which displays anticooperative behavior to the RXR ligand 9-cis retinoic acid (9C). In contrast to this anticooperative behavior, 9C has been shown to increase the activity of TR:RXR. Here we probed the influence of the affinity and the interactions of the TR ligand to the allostery of the TR:RXR through contact dynamics and residue networks. The TR ligand analogs were designed to have higher (G2) and lower (N1) binding energies than T3 when docked to the TR:RXR(9C) complex. The aqueous TR(N1/T3/G2):RXR(9C) complexes were subjected to 30 ns all-atom simulations using theNAMD. The program CAMERRA was used to capture the subtle perturbations of TR:RXR by mapping the residue contact dynamics. Various parts of the TR ligands; including the hydrophilic head, the iodine substituents, and the ligand tail; have been probed for their significance in ligand affinity. The results on the T3 and G2 complexes suggest that ligand affinity can be utilized as a predictor for anticooperative systems on which ligand is more likely to dissociate or remain bound. All 3 complexes also display distinct contact networks for cross-dimer signalling and ligand communication. Understanding ligand-based allostery could potentially unveil secrets of ligand-regulated protein dynamics, a foundation for the design of better and more efficient allosteric drugs.
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Affiliation(s)
- James Peter L Lim
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Mac Kevin E Braza
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines.
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16
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Rational Computational Design of Fourth-Generation EGFR Inhibitors to Combat Drug-Resistant Non-Small Cell Lung Cancer. Int J Mol Sci 2020; 21:ijms21239323. [PMID: 33297461 PMCID: PMC7730458 DOI: 10.3390/ijms21239323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Although the inhibitors of singly mutated epidermal growth factor receptor (EGFR) kinase are effective for the treatment of non-small cell lung cancer (NSCLC), their clinical efficacy has been limited due to the emergence of various double and triple EGFR mutants with drug resistance. It has thus become urgent to identify potent and selective inhibitors of triple mutant EGFRs resistant to first-, second-, and third-generation EGFR inhibitors. Herein, we report the discovery of potent and highly selective inhibitors of EGFR exon 19 p.E746_A750del/EGFR exon 20 p.T790M/EGFR exon 20 p.C797S (d746-750/T790M/C797S) mutant, which were derived via two-track virtual screening and de novo design. This two-track approach was performed so as to maximize and minimize the inhibitory activity against the triple mutant and the wild type, respectively. Extensive chemical modifications of the initial hit compounds led to the identification of several low-nanomolar inhibitors of the d746-750/T790M/C797S mutant. Among them, two compounds exhibited more than 104-fold selectivity in the inhibition of EGFRd746-750/T790M/C797S over the wild type. The formations of a hydrogen bond with the mutated residue Ser797 and the van der Waals contact with the mutated residue Met790 were found to be a common feature in the interactions between EGFRd746-750/T790M/C797S and the fourth-generation inhibitors. Such an exceptionally high selectivity could also be attributed to the formation of the hydrophobic contact with a Gly loop residue or the hydrogen bond with Asp855 in the activation loop. The discovery of the potent and selective EGFRd746-750/T790M/C797S inhibitors were actually made possible by virtue of the modified protein-ligand binding free energy function involving a new hydration free energy term with enhanced accuracy. The fourth-generation EGFR inhibitors found in this work are anticipated to serve as a new starting point for the discovery of anti-NSCLC medicines to overcome the problematic drug resistance.
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17
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Raček T, Schindler O, Toušek D, Horský V, Berka K, Koča J, Svobodová R. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res 2020; 48:W591-W596. [PMID: 32402071 PMCID: PMC7319571 DOI: 10.1093/nar/gkaa367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/16/2022] Open
Abstract
Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.
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Affiliation(s)
- Tomáš Raček
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic.,Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Ondřej Schindler
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Dominik Toušek
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Vladimír Horský
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc 771 46, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
| | - Radka Svobodová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 602 00, Czech Republic
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18
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Wu W, Li S, Yang M, Lin Y, Zheng K, Akutse KS. Citronellal perception and transmission by Anopheles gambiae s.s. (Diptera: Culicidae) females. Sci Rep 2020; 10:18615. [PMID: 33122679 PMCID: PMC7596511 DOI: 10.1038/s41598-020-75782-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/14/2020] [Indexed: 11/08/2022] Open
Abstract
Anopheles gambiae s.s. is a key vector of Plasmodium parasites. Repellents, which may be a promising alternative to pesticides used to control malaria mosquitoes. Although citronellal is a known mosquito repellent, its repellency characteristics are largely unknown. Determining the specific odorant-binding proteins (OBPs) and odorant receptors (ORs) that detect and transfer the citronellal molecule in A. gambiae s.s. will help to define the mode of action of this compound. In this research, we assessed the repellent activity of citronellal in A. gambiae s.s. using a Y-tube olfactory meter, screened candidate citronellal-binding OBPs and ORs using reverse molecular docking, clarified the binding properties of predicted proteins for citronellal using fluorescence competition binding assay. Results showed that citronellal had a dosage effect on repelling A. gambiae s.s.. The 50% repellent rate was determined to be 4.02 nmol. Results of simulated molecular docking showed that the only proteins that bound tightly with citronellal were AgamOBP4 and AgamORC7. Fluorescence competitive binding assays confirmed the simulations. This research determined that citronellal was captured by AgamOBP4 and transmitted to AgamORC7 in A. gambiae s.s.. Our study will be beneficial in the further understanding the repellent mechanism of citronellal against A. gambiae s.s..
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Affiliation(s)
- Weijian Wu
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Shanshan Li
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Min Yang
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Yongwen Lin
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China.
| | - Kaibin Zheng
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Komivi Senyo Akutse
- International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
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19
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Interleukin-26 activates macrophages and facilitates killing of Mycobacterium tuberculosis. Sci Rep 2020; 10:17178. [PMID: 33057074 PMCID: PMC7558018 DOI: 10.1038/s41598-020-73989-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis-causing Mycobacterium tuberculosis (Mtb) is transmitted via airborne droplets followed by a primary infection of macrophages and dendritic cells. During the activation of host defence mechanisms also neutrophils and T helper 1 (TH1) and TH17 cells are recruited to the site of infection. The TH17 cell-derived interleukin (IL)-17 in turn induces the cathelicidin LL37 which shows direct antimycobacterial effects. Here, we investigated the role of IL-26, a TH1- and TH17-associated cytokine that exhibits antimicrobial activity. We found that both IL-26 mRNA and protein are strongly increased in tuberculous lymph nodes. Furthermore, IL-26 is able to directly kill Mtb and decrease the infection rate in macrophages. Binding of IL-26 to lipoarabinomannan might be one important mechanism in extracellular killing of Mtb. Macrophages and dendritic cells respond to IL-26 with secretion of tumor necrosis factor (TNF)-α and chemokines such as CCL20, CXCL2 and CXCL8. In dendritic cells but not in macrophages cytokine induction by IL-26 is partly mediated via Toll like receptor (TLR) 2. Taken together, IL-26 strengthens the defense against Mtb in two ways: firstly, directly due to its antimycobacterial properties and secondly indirectly by activating innate immune mechanisms.
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20
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Durojaye OA, Mushiana T, Uzoeto HO, Cosmas S, Udowo VM, Osotuyi AG, Ibiang GO, Gonlepa MK. Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020; 21:44. [PMID: 38624499 PMCID: PMC7529470 DOI: 10.1186/s43042-020-00081-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background The 2019-nCoV which is regarded as a novel coronavirus is a positive-sense single-stranded RNA virus. It is infectious to humans and is the cause of the ongoing coronavirus outbreak which has elicited an emergency in public health and a call for immediate international concern has been linked to it. The coronavirus main proteinase which is also known as the 3C-like protease (3CLpro) is a very important protein in all coronaviruses for the role it plays in the replication of the virus and the proteolytic processing of the viral polyproteins. The resultant cytotoxic effect which is a product of consistent viral replication and proteolytic processing of polyproteins can be greatly reduced through the inhibition of the viral main proteinase activities. This makes the 3C-like protease of the coronavirus a potential and promising target for therapeutic agents against the viral infection. Results This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Comparative physiochemical studies were carried out on the resultant target protein and its template while selected HIV protease inhibitors were docked against the protein binding sites which contained no co-crystallized ligand. Conclusion In line with results from this study which has shown great consistency with other scientific findings on coronaviruses, we recommend the administration of the selected HIV protease inhibitors as first-line therapeutic agents for the treatment of the current coronavirus epidemic.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- School of Life Sciences, Department of Molecular and Cell Biology, University of Science and Technology of China, Hefei, China
- Department of Biochemistry, University of Nigeria, Nsukka, Enugu State Nigeria
- Department of Chemical Sciences, Coal City University, Emene, Enugu State Nigeria
| | - Talifhani Mushiana
- School of Chemistry and Material Sciences, Department of Chemistry, University of Science and Technology of China, Hefei, China
| | | | - Samuel Cosmas
- Department of Biochemistry, University of Nigeria, Nsukka, Enugu State Nigeria
| | | | - Abayomi Gaius Osotuyi
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Glory Omini Ibiang
- Department of Biological Sciences, Coal City University, Emene, Enugu State Nigeria
| | - Miapeh Kous Gonlepa
- School of Public Affairs, Department of Public Administration, University of Science and Technology of China, Hefei, China
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21
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Zhu F, Zhang X, Allen JE, Jones D, Lightstone FC. Binding Affinity Prediction by Pairwise Function Based on Neural Network. J Chem Inf Model 2020; 60:2766-2772. [PMID: 32338892 DOI: 10.1021/acs.jcim.0c00026] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a new approach to estimate the binding affinity from given three-dimensional poses of protein-ligand complexes. In this scheme, every protein-ligand atom pair makes an additive free-energy contribution. The sum of these pairwise contributions then gives the total binding free energy or the logarithm of the dissociation constant. The pairwise contribution is calculated by a function implemented via a neural network that takes the properties of the two atoms and their distance as input. The pairwise function is trained using a portion of the PDBbind 2018 data set. The model achieves good accuracy for affinity predictions when evaluated with PDBbind 2018 and with the CASF-2016 benchmark, comparing favorably to many scoring functions such as that of AutoDock Vina. The framework here may be extended to incorporate other factors to further improve its accuracy and power.
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Affiliation(s)
- Fangqiang Zhu
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Xiaohua Zhang
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Jonathan E Allen
- Global Security, Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Derek Jones
- Global Security, Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Felice C Lightstone
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
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22
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Bera P, Aher A, Brandao P, Manna SK, Mondal G, Jana A, Santra A, Jana H, Bera P. Induced apoptosis against U937 cancer cells by Fe(II), Co(III) and Ni(II) complexes with a pyrazine-thiazole ligand: Synthesis, structure and biological evaluation. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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New cyclometalated gold (III) complex targeting thioredoxin reductase: exploring as cytotoxic agents and mechanistic insights. Biometals 2020; 33:107-122. [DOI: 10.1007/s10534-020-00235-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
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24
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Phenanthridine derivatives as promising new anticancer agents: synthesis, biological evaluation and binding studies. Future Med Chem 2020; 12:709-739. [PMID: 32208986 DOI: 10.4155/fmc-2019-0016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Phenanthridines are an essential class of nitrogenous heterocycles with extensive applications in medicinal chemistry. The development of efficient and eco-friendly methods for the preparation of chirally pure dihydropyrrolo[1,2-f]phenanthridines (5a-h), and their in vitro evaluation and modeling studies as potential anticancer, antioxidant and DNA cleavage agents is reported. Methodology & results: Compounds 5a-h were prepared through a facile one-pot synthesis and characterized by infrared, high resolution mass spectrometry, 1H and 13C nuclear magnetic resonance. The molecules were subjected to virtual screening and docking analysis against selected human molecular targets. Compound 5g displayed good binding properties as well as significant anticancer and DNA cleavage activity. Conclusion: Compound 5g has been identified as a potential lead candidate for further testing against additional cancer cell lines and animal models in future.
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25
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Tabrizi L, Abyar F. Conjugation of a gold(iii) complex with vitamin B1 and chlorambucil derivatives: anticancer evaluation and mechanistic insights. Metallomics 2020; 12:721-731. [DOI: 10.1039/c9mt00304e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A gold(iii) complex containing vitamin B1 and chlorambucil derivatives was investigated for mechanistic insights in colon and breast cancer treatment.
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Affiliation(s)
- Leila Tabrizi
- School of Chemistry
- National University of Ireland, Galway
- Galway
- Ireland
| | - Fatemeh Abyar
- Department of Chemical Engineering
- Faculty of Engineering
- Ardakan University
- Ardakan
- Iran
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26
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Erdas-Cicek O, Atac AO, Gurkan-Alp AS, Buyukbingol E, Alpaslan FN. Three-Dimensional Analysis of Binding Sites for Predicting Binding Affinities in Drug Design. J Chem Inf Model 2019; 59:4654-4662. [PMID: 31596082 DOI: 10.1021/acs.jcim.9b00206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the interaction between drug molecules and proteins is one of the main challenges in drug design. Several tools have been developed recently to decrease the complexity of the process. Artificial intelligence and machine learning methods offer promising results in predicting the binding affinities. It becomes possible to do accurate predictions by using the known protein-ligand interactions. In this study, the electrostatic potential values extracted from 3-dimensional grid cubes of the drug-protein binding sites are used for predicting binding affinities of related complexes. A new algorithm with a dynamic feature selection method was implemented, which is derived from Compressed Images For Affinity Prediction (CIFAP) study, to predict binding affinities of Checkpoint Kinase 1 and Caspase 3 inhibitors.
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Affiliation(s)
- Ozlem Erdas-Cicek
- Department of Computer Engineering, Faculty of Engineering , Alanya Alaaddin Keykubat University , Alanya , 07425 Antalya , Turkey
| | - Ali Osman Atac
- Department of Computer Engineering , Middle East Technical University , Cankaya, 06800 Ankara , Turkey
| | - A Selen Gurkan-Alp
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Ankara University , Yenimahalle, 06560 Ankara , Turkey
| | - Erdem Buyukbingol
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Ankara University , Yenimahalle, 06560 Ankara , Turkey.,Pharmaceutical Chemistry, Faculty of Pharmacy , Afyonkarahisar Health Sciences University , 03200 Afyonkarahisar , Turkey
| | - Ferda Nur Alpaslan
- Department of Computer Engineering , Middle East Technical University , Cankaya, 06800 Ankara , Turkey
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27
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Adeoye AO, Olanlokun JO, Tijani H, Lawal SO, Babarinde CO, Akinwole MT, Bewaji CO. Molecular docking analysis of apigenin and quercetin from ethylacetate fraction of Adansonia digitata with malaria-associated calcium transport protein: An in silico approach. Heliyon 2019; 5:e02248. [PMID: 31687530 PMCID: PMC6819832 DOI: 10.1016/j.heliyon.2019.e02248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/20/2019] [Accepted: 08/05/2019] [Indexed: 11/29/2022] Open
Abstract
Background The investigation and knowledge of calcium handling mechanisms in the plasmodium has been considered as a potential biological target against malaria. Objective This study deals with the evaluation of inhibitory activity of secondary metabolites of ethylacetate partitioned-fraction of Adansonia digitata stem bark extract on malaria-associated protein using in silico docking studies. Materials and methods Molecular docking and virtual screening was performed to understand the mechanism of ligand binding and to identify potent calcium transporter inhibitors. The stem bark extracts of A. digitata contains rich sources of phytochemicals. The secondary metabolites were determined by HPLC-DAD and HRGC-MS analysis. The major chemical constituent present in the ethylacetate partitioned-fraction of A. digitata stem bark extract were examined for their antiplasmodial activity and were also involved in docking study. Results The secondary metabolites, quercetin and apigenin inhibited the formation of β-hematin. The results showed that all the selected compounds in the A. digitata showed binding energy ranging between -6.5 kcal/mol and -7.1 kcal/mol. Among the two chemical constituents, apigenin has the highest docking score along with the highest number of hydrogen bonds formed when compared to quercetin. Analysis of the results suggests that apigenin and quercetin could act as an anti-malaria agent. Conclusion Molecular docking analysis could lead to further development of potent calcium transporter inhibitors for the prevention and treatment of malaria and related conditions.
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Affiliation(s)
- Akinwunmi O Adeoye
- Department of Biochemistry, Federal University Oye Ekiti, Ekiti State, Nigeria.,Department of Biochemistry, University of Ilorin, Kwara State, Nigeria
| | - John O Olanlokun
- Biomembrane and Biotechnology Laboratory, Department of Biochemistry, University of Ibadan, Oyo State, Nigeria
| | - Habib Tijani
- Department of Biochemistry, University of Ilorin, Kwara State, Nigeria
| | - Segun O Lawal
- Biomembrane and Biotechnology Laboratory, Department of Biochemistry, University of Ibadan, Oyo State, Nigeria
| | - Cecilia O Babarinde
- Biomembrane and Biotechnology Laboratory, Department of Biochemistry, University of Ibadan, Oyo State, Nigeria
| | - Mobolaji T Akinwole
- Biomembrane and Biotechnology Laboratory, Department of Biochemistry, University of Ibadan, Oyo State, Nigeria
| | - Clement O Bewaji
- Department of Biochemistry, University of Ilorin, Kwara State, Nigeria
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28
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Yeon Kim B, Hee Yoon J, Kim M, Nyoung Kim J, Park H, Eon Ryu S, Lee S. Synthesis and biological evaluation of acylthiourea against DUSP1 inhibition. Bioorg Med Chem Lett 2019; 29:1746-1748. [PMID: 31103445 DOI: 10.1016/j.bmcl.2019.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 01/29/2023]
Abstract
Structure based virtual screening attempts to discover DUSP1 inhibitors have yielded a scaffold featuring benzoxazole and acylthiourea pharmacophore. A series of its analogues were synthesized to explore structure activity relationship (SAR) of DUSP1 inhibition.
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Affiliation(s)
- Bo Yeon Kim
- Anticancer Agent Research Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Ji Hee Yoon
- Anticancer Agent Research Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Myeongbin Kim
- Department of Bioengineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Jae Nyoung Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Seong Eon Ryu
- Department of Bioengineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Sangku Lee
- Anticancer Agent Research Center, KRIBB, Cheongju 28116, Republic of Korea.
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29
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Mechanistic and Conformational Studies on the Interaction Between Myriocin and Human Serum Albumin by Fluorescence Spectroscopy and Molecular Docking. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Abyar F, Tabrizi L. Experimental and theoretical investigations of novel oxidovanadium(IV) juglone complex: DNA/HSA interaction and cytotoxic activity. J Biomol Struct Dyn 2019; 38:474-487. [PMID: 30831056 DOI: 10.1080/07391102.2019.1580221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A new oxidovanadium(IV) complex VO(L)(Jug) (HL = 5-methoxy-1,3-bis (1-methyl-1H-benzo[d]imidazol-2-yl)benzene, Jug = juglone) was synthesized and characterized. Interactions of the V(IV) complex with calf thymus DNA (CT DNA) and human serum albumin were studied using different techniques such as UV-vis and fluorescence emission spectroscopy. The experimental results were confirmed by the molecular docking study. The oxidovanadium(IV) complex can efficiently cleave pUC19 DNA in the presence of Hydrogen peroxide. Also, the in vitro cytotoxicity properties of the oxidovanadium(IV) complex was evaluated against MCF-7, HPG-2 and HT-29 cancer cell lines and HEK293 non-malignant fibroblasts were evaluated and compared with free ligands, VOSO4 and cisplatin as reference drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatemeh Abyar
- Department of Chemical Engineering, Faculty of Engineering, Ardakan University, Ardakan, Iran
| | - Leila Tabrizi
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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Zheng S, Yang S, Cheng X, Bau T, Li Y, Zhang R, Bao H. Fluorescence Spectroscopy and Molecular Docking Approach to Probe the Interaction between Dehydroeburicoic Acid and Human Serum Albumin. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/aim.2019.91003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dhusia K, Raja K, Thomas PPM, Yadav PK, Ramteke PW. Molecular dynamics simulation analysis of conessine against multi drug resistant Serratia marcescens. INFECTION GENETICS AND EVOLUTION 2018; 67:101-111. [PMID: 30396000 DOI: 10.1016/j.meegid.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/02/2018] [Accepted: 11/01/2018] [Indexed: 10/27/2022]
Abstract
Ornithine decarboxylase (ODC) is an immediate precursor of polyamine biosynthesis in Serratia marcescens and a potential target for inhibition of its growth. We predicted the 3D structural conformation of ODC enzyme and validated it using MDS in our previous study. In this current study, the potential inhibitors of ODC were obtained by virtual screening of potential inhibitors from ZINC database and studied in depth for their different binding pose. Among the ten virtually screened inhibitors, Conessine exhibited the best binding with ODC and its inhibition property was studied further by MDS studies. The natural compound conessine is isolated from plant Holarrhena antidysenterica and it is studied against ODC of Serratia marcenses for its inhibitory potentials. This revealed unforeseen twisted position in root mean square fluctuation (RMSF) and ODC modelled conformation that influenced ligand binding. Both predicted model and ligand bound model were compared and found to be stable with Root Mean Square Deviation (RMSD) of approximately 7 nm and 0.25 nm to that of crystallographic structure over simulation time of 55 ns and 70 ns respectively. This work paves the way for future development of new drugs against nosocomial diseases caused by Serratia marcescens.
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Affiliation(s)
- Kalyani Dhusia
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India
| | - Kalpana Raja
- Department of Dermatology, University of Michigan Medical School, Ann arbor, MI 48109, USA
| | - Pierre Paul Michel Thomas
- Institute of Public Health Genomics, Genetics and Cell Biology cluster, GROW Research School for Oncology and Developmental Biology, Maastricht University, the Netherlands
| | - Pramod K Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India
| | - Pramod W Ramteke
- Department of Biological Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India.
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Zhang L, Yuan Y, Ren T, Guo Y, Li C, Pu X. Shining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor. Sci Rep 2018; 8:7824. [PMID: 29777138 PMCID: PMC5959861 DOI: 10.1038/s41598-018-26105-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Olfactory receptor (OR)-based bioelectronic nose is a new type of bio-affinity sensor applied for detecting numerous odorant molecules. In order to elucidate the effect of the adsorption of nanomaterial carriers on the receptor structure and its selectivity to odors, we used a systematic computation-scheme to study two OR models immobilized onto carbon nanotube. Our result indicates that there is a multistep OR-adsorption process driven by hydrophobic interaction. Many allosteric communication pathways exist between the absorbed residues and the pocket ones, leading to a significant shrinkage of the pocket. Consequently, the size-selectivity of the receptor to the odors is changed to some extent. But, the odor size and its hydrophobicity, rather than specific functional groups of the odor, still play a determinant role in binding OR, at least for the 132 odors under study. Regardless of the limitation for the odor size in initial recognition, the different-size odors could induce significant changes in the pocket conformation so that it could better match the pocket space, indicating the importance of the ligand-fit binding. Due to the CNT-induced shrinkage of the pocket, the CNT immobilization could increase the binding affinity through enhancing van der Waals interaction, in particular for the large odors.
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Affiliation(s)
- Liyun Zhang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu, 610041, P.R. China
| | - Tian Ren
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, 610064, P.R. China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China.
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Dey A, Kamat A, Nayak S, Danino D, Kesselman E, Dandekar P, Jain R. Role of proton balance in formation of self-assembled chitosan nanoparticles. Colloids Surf B Biointerfaces 2018; 166:127-134. [PMID: 29558703 DOI: 10.1016/j.colsurfb.2018.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 11/17/2022]
Abstract
Researchers have explored the ability of chitosan to form nanoparticles, to suit varying applications, ranging from wound-healing to gene delivery. Ionic gelation is a widely used method for formulating chitosan nanoparticles, where self-assembly plays a crucial role. This self-assembly is initially promoted by hydrophilic-hydrophobic parity amongst individual chitosan residues, along with electrostatic and Van der Waals interactions with the cross-linker. However, until now the intrinsic ability of chitosan to self-assemble is not widely studied; hence, we investigate the self-assembly of chitosan, based on proton balance between its protonated and deprotonated residues, to promote facile nanoparticle synthesis. This is one of the first reports that highlights subtle but critical influence of proton balance in the chitosan polymer on the formation of chitosan nanoparticles.
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Affiliation(s)
- Anomitra Dey
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Aditya Kamat
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Sonal Nayak
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Dganit Danino
- Department of Biotechnology & Food Engineering, Technion - Israel Institute of Technology, Hafia 3200003, Israel
| | - Ellina Kesselman
- Department of Biotechnology & Food Engineering, Technion - Israel Institute of Technology, Hafia 3200003, Israel
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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35
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Amperayani KR, Kumar KN, Parimi UD. Synthesis and in vitro and in silico antimicrobial studies of novel piperine–pyridine analogs. RESEARCH ON CHEMICAL INTERMEDIATES 2018. [DOI: 10.1007/s11164-018-3324-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Heinrich JC, Donakonda S, Haupt VJ, Lennig P, Zhang Y, Schroeder M. New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells. Oncotarget 2018; 7:68156-68169. [PMID: 27626687 PMCID: PMC5356546 DOI: 10.18632/oncotarget.11905] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/26/2016] [Indexed: 12/13/2022] Open
Abstract
Drug resistance is an important open problem in cancer treatment. In recent years, the heat shock protein HSP27 (HSPB1) was identified as a key player driving resistance development. HSP27 is overexpressed in many cancer types and influences cellular processes such as apoptosis, DNA repair, recombination, and formation of metastases. As a result cancer cells are able to suppress apoptosis and develop resistance to cytostatic drugs. To identify HSP27 inhibitors we follow a novel computational drug repositioning approach. We exploit a similarity between a predicted HSP27 binding site to a viral thymidine kinase to generate lead inhibitors for HSP27. Six of these leads were verified experimentally. They bind HSP27 and down-regulate its chaperone activity. Most importantly, all six compounds inhibit development of drug resistance in cellular assays. One of the leads – chlorpromazine – is an antipsychotic, which has a positive effect on survival time in human breast cancer. In summary, we make two important contributions: First, we put forward six novel leads, which inhibit HSP27 and tackle drug resistance. Second, we demonstrate the power of computational drug repositioning.
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Affiliation(s)
- Jörg C Heinrich
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sainitin Donakonda
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - V Joachim Haupt
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Petra Lennig
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
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Park H, Jung HY, Mah S, Hong S. Systematic Computational Design and Identification of Low Picomolar Inhibitors of Aurora Kinase A. J Chem Inf Model 2018; 58:700-709. [DOI: 10.1021/acs.jcim.7b00671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
| | - Hoi-Yun Jung
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141, Korea
| | - Shinmee Mah
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141, Korea
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38
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Iraji A, Firuzi O, Khoshneviszadeh M, Tavakkoli M, Mahdavi M, Nadri H, Edraki N, Miri R. Multifunctional iminochromene-2H-carboxamide derivatives containing different aminomethylene triazole with BACE1 inhibitory, neuroprotective and metal chelating properties targeting Alzheimer's disease. Eur J Med Chem 2017; 141:690-702. [PMID: 29107423 DOI: 10.1016/j.ejmech.2017.09.057] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 01/26/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder known for the presence of amyloid beta plaques resulting from the sequential action of β-secretase and γ-secretase on amyloid precursor protein. We developed and synthesized, through click reactions, a new family of iminochromene carboxamides containing different aminomethylene triazole. The BACE1 inhibition, neuroprotective capacity and metal chelation of these derivatives make them ideal candidates against AD. Most of the synthesized compounds were shown to have potent BACE1 inhibitory activity in a FRET assay, with an IC50 value of 2.2 μM for the most potent compound. Moreover, molecular modeling evaluation of these BACE1 inhibitors demonstrates the vital role of the amine and amide linkers through hydrogen bond interactions with key amino acids in the BACE1 active site. Our in vitro neuroprotective evaluations in PC12 neuronal cells of Aβ-induced neuroprotection demonstrated promising activity for most of the compounds as neuroprotective agents. Based on our findings, we propose that introduction of a phthalimide substitute on the triazole ring shown to be interesting multifunctional lead compound worthy of further study.
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Affiliation(s)
- Aida Iraji
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marjan Tavakkoli
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Nadri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ramin Miri
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Park H, Lee HS, Ku B, Lee SR, Kim SJ. Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1. J Comput Aided Mol Des 2017; 31:743-753. [PMID: 28653253 DOI: 10.1007/s10822-017-0037-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/20/2017] [Indexed: 11/29/2022]
Abstract
Despite a wealth of persuasive evidence for the involvement of human small C-terminal domain phosphatase 1 (Scp1) in the impairment of neuronal differentiation and in Huntington's disease, small-molecule inhibitors of Scp1 have been rarely reported so far. This study aims to the discovery of both competitive and allosteric Scp1 inhibitors through the two-track virtual screening procedure. By virtue of the improvement of the scoring function by implementing a new molecular solvation energy term and by reoptimizing the atomic charges for the active-site Mg2+ ion cluster, we have been able to identify three allosteric and five competitive Scp1 inhibitors with low-micromolar inhibitory activity. Consistent with the results of kinetic studies on the inhibitory mechanisms, the allosteric inhibitors appear to be accommodated in the peripheral binding pocket through the hydrophobic interactions with the nonpolar residues whereas the competitive ones bind tightly in the active site with a direct coordination to the central Mg2+ ion. Some structural modifications to improve the biochemical potency of the newly identified inhibitors are proposed based on the binding modes estimated with docking simulations.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, South Korea.
| | - Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju, 28116, South Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
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Dostani M, Kianfar AH, Mahmood WAK, Dinari M, Farrokhpour H, Sabzalian MR, Abyar F, Azarian MH. An experimental and theoretical study on the interaction of DNA and BSA with novel Ni 2+, Cu 2+ and VO 2+ complexes derived from vanillin bidentate Schiff base ligand. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 180:144-153. [PMID: 28284160 DOI: 10.1016/j.saa.2017.02.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
In this investigation, the structure of bidentate N,N-Schiff base ligand of vanillin, (E)-4-(((2-amino-5-nitrophenyl)imino)methyl)-2-methoxyphenol (HL) was determined by single crystal X-ray diffraction. The interaction of new [CuL2], [NiL2] and [VOL2] complexes with DNA and BSA was explored through UV-Vis and fluorescence spectroscopy. The electronic spectra changes displayed an isosbestic point for the complexes upon titration with DNA. The Kb values for the complexes [CuL2], [NiL2] and [VOL2] were 2.4×105, 1.9×105 and 4.2×104, respectively. [CuL2] complex was bound more toughly than [NiL2] and [VOL2] complexes. These complexes had a significant interaction with Bovine Serum Albumin (BSA) and the results demonstrated that the quenching mechanism was a static procedure. Also, the complexes interacted with BSA by more than one binding site (n>1). Finally, the theoretical studies were performed using the docking method to calculate the binding constants and recognize the binding site of the DNA and BSA with the complexes. The ligand and complexes including Ni2+, Cu2+ and VO2+ ions were colonized by fungal growth.
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Affiliation(s)
- Morteza Dostani
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Ali Hossein Kianfar
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran.
| | | | - Mohammad Dinari
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Mohammad R Sabzalian
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Fatemeh Abyar
- Department of Engineering, Ardakan University, Ardakan 89518-95491, Iran
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Giełdoń A, Witt MM, Gajewicz A, Puzyn T. Rapid insight into C60 influence on biological functions of proteins. Struct Chem 2017. [DOI: 10.1007/s11224-017-0957-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Docking and molecular dynamics studies on triclosan derivatives binding to FabI. J Mol Model 2017; 23:25. [DOI: 10.1007/s00894-016-3192-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
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43
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Zhang L, Li Y, Yuan Y, Jiang Y, Guo Y, Li M, Pu X. Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media. Sci Rep 2016; 6:36838. [PMID: 27874101 PMCID: PMC5118797 DOI: 10.1038/srep36838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/17/2016] [Indexed: 02/04/2023] Open
Abstract
In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.
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Affiliation(s)
- Liyun Zhang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuzhi Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, People's Republic of China
| | - Yuanyuan Jiang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
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Raček T, Pazúriková J, Svobodová Vařeková R, Geidl S, Křenek A, Falginella FL, Horský V, Hejret V, Koča J. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J Cheminform 2016; 8:57. [PMID: 27803746 PMCID: PMC5067907 DOI: 10.1186/s13321-016-0171-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/05/2016] [Indexed: 11/21/2022] Open
Abstract
Background The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equalization method (EEM) is the most frequently used approach for calculating partial atomic charges. EEM is fast and its accuracy is comparable to the quantum mechanical charge calculation method for which it was parameterized. Several EEM parameter sets for various types of molecules and QM charge calculation approaches have been published and new ones are still needed and produced. Methodologies for EEM parameterization have been described in a few articles, but a software tool for EEM parameterization and EEM parameter sets validation has not been available until now. Results We provide the software tool NEEMP (http://ncbr.muni.cz/NEEMP), which offers three main functionalities: EEM parameterization [via linear regression (LR) and differential evolution with local minimization (DE-MIN)]; EEM parameter set validation (i.e., validation of coverage and quality) and EEM charge calculation. NEEMP functionality is shown using a parameterization and a validation case study. The parameterization case study demonstrated that LR is an appropriate approach for smaller and homogeneous datasets and DE-MIN is a suitable solution for larger and heterogeneous datasets. The validation case study showed that EEM parameter set coverage and quality can still be problematic. Therefore, it makes sense to verify the coverage and quality of EEM parameter sets before their use, and NEEMP is an appropriate tool for such verification. Moreover, it seems from both case studies that new EEM parameterizations need to be performed and new EEM parameter sets obtained with high quality and coverage for key structural databases. Conclusion We provide the software tool NEEMP, which is to the best of our knowledge the only available software package that enables EEM parameterization and EEM parameter set validation. Additionally, its DE-MIN parameterization method is an innovative approach, developed by ourselves and first published in this work. In addition, we also prepared four high-quality EEM parameter sets tailored to ligand molecules.. ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0171-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomáš Raček
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Jana Pazúriková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislav Geidl
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aleš Křenek
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; Institute of Computer Science, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Francesco Luca Falginella
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vladimír Horský
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Václav Hejret
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic ; National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
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Seol JH, Song TY, Oh SE, Jo C, Choi A, Kim B, Park J, Hong S, Song I, Jung KY, Yang JH, Park H, Ahn JH, Han JW, Cho EJ. Identification of small molecules that inhibit the histone chaperone Asf1 and its chromatin function. BMB Rep 2016; 48:685-90. [PMID: 26058396 PMCID: PMC4791324 DOI: 10.5483/bmbrep.2015.48.12.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/01/2022] Open
Abstract
The eukaryotic genome is packed into chromatin, which is important for the genomic integrity and gene regulation. Chromatin structures are maintained through assembly and disassembly of nucleosomes catalyzed by histone chaperones. Asf1 (anti-silencing function 1) is a highly conserved histone chaperone that mediates histone transfer on/off DNA and promotes histone H3 lysine 56 acetylation at globular core domain of histone H3. To elucidate the role of Asf1 in the modulation of chromatin structure, we screened and identified small molecules that inhibit Asf1 and H3K56 acetylation without affecting other histone modifications. These pyrimidine-2,4,6-trione derivative molecules inhibited the nucleosome assembly mediated by Asf1 in vitro, and reduced the H3K56 acetylation in HeLa cells. Furthermore, production of HSV viral particles was reduced by these compounds. As Asf1 is implicated in genome integrity, cell proliferation, and cancer, current Asf1 inhibitor molecules may offer an opportunity for the therapeutic development for treatment of diseases. [BMB Reports 2015; 48(12): 685-690]
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Affiliation(s)
- Ja-Hwan Seol
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Tae-Yang Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Se Eun Oh
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Chanhee Jo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Ahreum Choi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Byungho Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Jinyoung Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Suji Hong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Ilrang Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Kwan Young Jung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Jae-Hyun Yang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul 05006, Korea
| | - Jin-Hyun Ahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Eun-Jung Cho
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
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Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures. Drug Discov Today 2016; 21:1672-1680. [DOI: 10.1016/j.drudis.2016.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
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Kadioglu O, Efferth T. Peptide aptamer identified by molecular docking targeting translationally controlled tumor protein in leukemia cells. Invest New Drugs 2016; 34:515-21. [DOI: 10.1007/s10637-016-0339-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/04/2016] [Indexed: 11/29/2022]
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Zheng F, Robertson AP, Abongwa M, Yu EW, Martin RJ. The Ascaris suum nicotinic receptor, ACR-16, as a drug target: Four novel negative allosteric modulators from virtual screening. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2016; 6:60-73. [PMID: 27054065 PMCID: PMC4805779 DOI: 10.1016/j.ijpddr.2016.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/28/2016] [Accepted: 02/05/2016] [Indexed: 12/22/2022]
Abstract
Soil-transmitted helminth infections in humans and livestock cause significant debility, reduced productivity and economic losses globally. There are a limited number of effective anthelmintic drugs available for treating helminths infections, and their frequent use has led to the development of resistance in many parasite species. There is an urgent need for novel therapeutic drugs for treating these parasites. We have chosen the ACR-16 nicotinic acetylcholine receptor of Ascaris suum (Asu-ACR-16), as a drug target and have developed three-dimensional models of this transmembrane protein receptor to facilitate the search for new bioactive compounds. Using the human α7 nAChR chimeras and Torpedo marmorata nAChR for homology modeling, we defined orthosteric and allosteric binding sites on the Asu-ACR-16 receptor for virtual screening. We identified four ligands that bind to sites on Asu-ACR-16 and tested their activity using electrophysiological recording from Asu-ACR-16 receptors expressed in Xenopus oocytes. The four ligands were acetylcholine inhibitors (SB-277011-A, IC50, 3.12 ± 1.29 μM; (+)-butaclamol Cl, IC50, 9.85 ± 2.37 μM; fmoc-1, IC50, 10.00 ± 1.38 μM; fmoc-2, IC50, 16.67 ± 1.95 μM) that behaved like negative allosteric modulators. Our work illustrates a structure-based in silico screening method for seeking anthelmintic hits, which can then be tested electrophysiologically for further characterization. Three-dimensional structural models of the Ascaris nicotinic (Asu-ACR-16) receptor made by homology modeling. High affinity ligands selected by in silico screening. Four ligands validated by electrophysiological studies as negative allosteric modulators.
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Affiliation(s)
- Fudan Zheng
- Department of Chemistry, College of Liberal Arts and Sciences, Iowa State University, Ames, IA 50011, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Melanie Abongwa
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Edward W Yu
- Department of Chemistry, College of Liberal Arts and Sciences, Iowa State University, Ames, IA 50011, USA; Department of Physics and Astronomy, College of Liberal Arts and Sciences, Iowa State University, Ames, IA 50011, USA
| | - Richard J Martin
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
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SAENGLEE S, JOGLOY S, PATANOTHAI A, SENAWONG T. Cytotoxic effects of peanut phenolic compounds possessing histone deacetylase inhibitory activity on human colon cancer cell lines. Turk J Biol 2016. [DOI: 10.3906/biy-1601-23] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J. High-quality and universal empirical atomic charges for chemoinformatics applications. J Cheminform 2015; 7:59. [PMID: 26633997 PMCID: PMC4667495 DOI: 10.1186/s13321-015-0107-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charges perform very successfully. In particular, their fast and accurate calculation via the Electronegativity Equalization Method (EEM) seems very promising for chemoinformatics applications. Unfortunately, published EEM parameter sets include only parameters for basic atom types and they often miss parameters for halogens, phosphorus, sulphur, triple bonded carbon etc. Therefore their applicability for drug-like molecules is limited. RESULTS We have prepared six EEM parameter sets which enable the user to calculate EEM charges in a quality comparable to quantum mechanics (QM) charges based on the most common charge calculation schemes (i.e., MPA, NPA and AIM) and a robust QM approach (HF/6-311G, B3LYP/6-311G). The calculated EEM parameters exhibited very good quality on a training set ([Formula: see text]) and also on a test set ([Formula: see text]). They are applicable for at least 95 % of molecules in key drug databases (DrugBank, ChEMBL, Pubchem and ZINC) compared to less than 60 % of the molecules from these databases for which currently used EEM parameters are applicable. CONCLUSIONS We developed EEM parameters enabling the fast calculation of high-quality partial atomic charges for almost all drug-like molecules. In parallel, we provide a software solution for their easy computation (http://ncbr.muni.cz/eem_parameters). It enables the direct application of EEM in chemoinformatics.
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Affiliation(s)
- Stanislav Geidl
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Bouchal
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Raček
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
- />Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Václav Hejret
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aleš Křenek
- />Institute of Computer Science, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Ruben Abagyan
- />Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive, San Diego, MC 0657 USA
| | - Jaroslav Koča
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
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