1
|
Agarwal R, Smith JC. Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina. Mol Inform 2023; 42:e2200188. [PMID: 36262028 DOI: 10.1002/minf.202200188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
Structure-based virtual high-throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e., the 'docking power'. Here, using a popular algorithm, Autodock Vina, as a model program, we evaluate the effects of varying two common docking parameters: the box size (the size of docking search space) and the exhaustiveness of the global search (the number of independent runs starting from random ligand conformations) on the RMSD from the PDBbind v2017 refined dataset of experimental protein-ligand complexes. Although it is clear that exhaustiveness is an important parameter, there is wide variation in the values used, with variation between 1 and >100. We, therefore, evaluated a combination of cubic boxes of different sizes and five exhaustiveness values (1, 8, 25, 50, 75, 100) within the range of those commonly adopted. The results show that the default exhaustiveness value of 8 performs well overall for most box sizes. In contrast, for all box sizes, but particularly for large boxes, an exhaustiveness value of 1 led to significantly higher median RMSD (mRMSD) values. The docking power was slightly improved with an exhaustiveness of 25, but the mRMSD changes little with values higher than 25. Therefore, although low exhaustiveness is computationally faster, the results are more likely to be far from reality, and, conversely, values >25 led to little improvement at the expense of computational resources. Overall, we recommend users to use at least the default exhaustiveness value of 8 for virtual screening calculations.
Collapse
Affiliation(s)
- Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6309, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 14311 Cumberland Avenue, Knoxville, TN 37996-1939, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6309, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 14311 Cumberland Avenue, Knoxville, TN 37996-1939, USA
| |
Collapse
|
2
|
Phylogenetic Studies and Metabolite Analysis of Sticta Species from Colombia and Chile by Ultra-High Performance Liquid Chromatography-High Resolution-Q-Orbitrap-Mass Spectrometry. Metabolites 2022; 12:metabo12020156. [PMID: 35208230 PMCID: PMC8875025 DOI: 10.3390/metabo12020156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
Eleven species of lichens of the genus Sticta, ten of which were collected in Colombia (S. pseudosylvatica S. luteocyphellata S. cf. andina S. cf. hypoglabra, S. cordillerana, S. cf. gyalocarpa S. leucoblepharis, S. parahumboldtii S. impressula, S. ocaniensis) and one collected in Chile (S. lineariloba), were analyzed for the first time using hyphenated liquid chromatography with high-resolution mass spectrometry. In the metabolomic analysis, a total of 189 peaks were tentatively detected; the analyses were divided in five (5) groups of compounds comprising lipids, small phenolic compounds, saturated acids, terpenes, and typical phenolic lichen compounds such as depsides, depsidones and anthraquinones. The metabolome profiles of these eleven species are important since some compounds were identified as chemical markers for the fast identification of Sticta lichens for the first time. Finally, the usefulness of chemical compounds in comparison to traditional morphological traits to the study of ancestor–descendant relationships in the genus was assessed. Chemical and morphological consensus trees were not consistent with each other and recovered different relationships between taxa.
Collapse
|
3
|
Iwasaki A, Tadenuma T, Sumimoto S, Shiota I, Matsubara T, Saito-Nakano Y, Nozaki T, Sato T, Suenaga K. Hoshinoamides A and B, Acyclic Lipopeptides from the Marine Cyanobacterium Caldora penicillata. JOURNAL OF NATURAL PRODUCTS 2018; 81:2545-2552. [PMID: 30387355 DOI: 10.1021/acs.jnatprod.8b00643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hoshinoamides A (1) and B (2), new acyclic lipopeptides, were isolated from the marine cyanobacterium Caldora penicillata. Their structures were elucidated by spectroscopic analyses and degradation reactions. Hoshinoamides A (1) and B (2) did not exhibit any cytotoxicity against HeLa cells at 10 μM, but inhibited the in vitro growth of the malarial parasite Plasmodium falciparum (IC50 = 0.52 and 1.0 μM, respectively).
Collapse
Affiliation(s)
- Arihiro Iwasaki
- Department of Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Takato Tadenuma
- Department of Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Shimpe Sumimoto
- Department of Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Ikuma Shiota
- Department of Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Yumiko Saito-Nakano
- Department of Parasitology , National Institute of Infectious Diseases , 1-23-1 Toyama, Shinjuku-ku , Tokyo 162-8640 , Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| |
Collapse
|
4
|
Liang Z, Li QX. Discovery of Selective, Substrate-Competitive, and Passive Membrane Permeable Glycogen Synthase Kinase-3β Inhibitors: Synthesis, Biological Evaluation, and Molecular Modeling of New C-Glycosylflavones. ACS Chem Neurosci 2018; 9:1166-1183. [PMID: 29381861 DOI: 10.1021/acschemneuro.8b00010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Glycogen synthase kinase-3β (GSK-3β) is a key enzyme responsible for tau hyperphosphorylation and is a viable therapeutic target of Alzheimer's disease (AD). We developed a new class of GSK-3β inhibitors based on the 6- C-glycosylflavone isoorientin (1). The new inhibitors are passive membrane permeable and constitutively attenuate GSK-3β mediated tau hyperphosphorylation and amyloid neurotoxicity in an AD cellular model. Enzymatic assays and kinetic studies demonstrated that compound 30 is a GSK-3β substrate-competitive inhibitor with distinct kinase selectivity, isoform-selectivity and over 310-fold increased potency as compared to 1. Structure-activity relationship analyses and in silico modeling suggest the mechanism of actions by which the hydrophobic, π-cation, and orthogonal multipolar interactions of 30 with the substrate site are critical for the GSK-3β inhibition and selectivity. The results provide new insights into GSK-3β drug discovery. The new inhibitors are valuable chemical probes and drug leads with therapeutic potential to tackle AD and other GSK-3β relevant diseases.
Collapse
Affiliation(s)
- Zhibin Liang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| |
Collapse
|
5
|
Shao LP, Si CM, Mao ZY, Zhou W, Molinski TF, Wei BG, Lin GQ. Synthesis and Structure Revision of Symplocin A. Org Chem Front 2017; 4:995-1004. [PMID: 31007934 DOI: 10.1039/c7qo00052a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Symplocin A, a linear peptide possessing N-terminal N,N-dimethylisoleucine, statine, and valic acid residues, has been synthesized for the first time employing our previously established 'one-pot intramolecular tandem protocol'. Moreover, the stereochemistry of natural symplocin A was unambiguously revised through the confirmation by 1D NMR, 2D NMR, and HPLC comparisons with authentic natural product.
Collapse
Affiliation(s)
- Lu-Ping Shao
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Chang-Mei Si
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Zhuo-Ya Mao
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Wen Zhou
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093-0358, United States
| | - Bang-Guo Wei
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Guo-Qiang Lin
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| |
Collapse
|
6
|
Elkobi-Peer S, Carmeli S. New prenylated aeruginosin, microphycin, anabaenopeptin and micropeptin analogues from a Microcystis bloom material collected in Kibbutz Kfar Blum, Israel. Mar Drugs 2015; 13:2347-75. [PMID: 25884445 PMCID: PMC4413215 DOI: 10.3390/md13042347] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 11/25/2022] Open
Abstract
Thirteen new and eighteen known natural products were isolated from a bloom material of an assembly of various Microcystis spp. collected in November, 2008, from a commercial fishpond near Kibbutz Kfar Blum, the Jordan Valley, Israel. The new natural products included the prenylated aeruginosin KB676 (1), microphycin KB921 (2), anabaenopeptins KB906 (3) and KB899 (4) and micropeptins KB928 (5), KB956 (6), KB970A (7), KB970B (8), KB984 (9), KB970C (10), KB1048 (11), KB992 (12) and KB1046 (13). Their structures were elucidated primarily by interpretation of their 1D and 2D nuclear magnetic resonance spectra and high-resolution mass spectrometry. Marfey's and chiral-phase high performance liquid chromatography methods were used to determine the absolute configurations of their chiral centers. Aeruginosin KB676 (1) contains the rare (2S,3aS,6S,7aS)-Choi and is the first prenylated aeruginosin derivative described in the literature. Compounds 1 and 5-11 inhibited trypsin with sub-μM IC50s, while Compounds 11-13 inhibited chymotrypsin with sub-μM IC50s. The structures and biological activities of the new natural products and our procedures of dereplication are described.
Collapse
Affiliation(s)
- Shira Elkobi-Peer
- Raymond and Beverly Sackler Faculty of Exact Sciences, Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| | - Shmuel Carmeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| |
Collapse
|
7
|
Li X, Li YL, Chen Y, Zou Y, Zhuo XB, Wu QY, Zhao QJ, Hu HG. A silver-promoted solid-phase guanidylation process enables the first total synthesis of stictamide A. RSC Adv 2015. [DOI: 10.1039/c5ra20976e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
First total synthesis of stictamide A, a structurally unique peptide with a statine motif and a N-prenyl modified arginine in the side chain, is disclosed with a novel silver-promoted solid-phase strategy for the first time.
Collapse
Affiliation(s)
- Xiang Li
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| | - Yu-lei Li
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| | - Yan Chen
- Department of Pharmacy
- General Hospital of Beijing Military Region
- Beijing 100700
- China
| | - Yan Zou
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| | - Xiao-bin Zhuo
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| | - Qiu-ye Wu
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| | - Qing-jie Zhao
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| | - Hong-gang Hu
- Department of Organic Chemistry
- School of Pharmacy
- Second Military Medical University
- Shanghai 200433
- China
| |
Collapse
|
8
|
Audoin C, Sánchez JA, Genta-Jouve G, Alfonso A, Rios L, Vale C, Thomas OP, Botana LM. Autumnalamide, a prenylated cyclic peptide from the cyanobacterium Phormidium autumnale, acts on SH-SY5Y cells at the mitochondrial level. JOURNAL OF NATURAL PRODUCTS 2014; 77:2196-2205. [PMID: 25265024 DOI: 10.1021/np500374a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Filamentous cyanobacteria of the genus Phormidium have been rarely studied for their chemical diversity. For the first time, the cultivable Phormidium autumnale was shown to produce a prenylated cyclic peptide named autumnalamide (1). The structure of this peptide was fully determined after a deep exploration of the spectroscopic data, including NMR and HRMS. Interestingly, a prenyl moiety was located on the guanidine end of the arginine amino acid. The absolute configurations of most amino acids were assessed using enantioselective GC/MS analysis, with (13)C NMR modeling being used for the determination of d-arginine and d-proline. The effects of 1 on sodium and calcium fluxes were studied in SH-SY5Y and hNav 1.6 HEK cells. When the Ca(2+) influx was stimulated by thapsigargin, strong inhibition was observed in the presence of 1. As a consequence, this compound may act by disrupting the normal calcium uptake of this organelle, inducing the opening of the mitochondrial permeability transition pore, which results in the indirect blockade of store-operated channels.
Collapse
Affiliation(s)
- Coralie Audoin
- Institut de Chimie de Nice-PCRE, UMR 7272 CNRS, Faculty of Science, University of Nice Sophia-Antipolis , Parc Valrose, 06108 Nice, France
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Um S, Pyee Y, Kim EH, Lee SK, Shin J, Oh DC. Thalassospiramide G, a new γ-amino-acid-bearing peptide from the marine bacterium Thalassospira sp. Mar Drugs 2013; 11:611-22. [PMID: 23442790 PMCID: PMC3705361 DOI: 10.3390/md11030611] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/29/2013] [Accepted: 02/06/2013] [Indexed: 01/05/2023] Open
Abstract
In the chemical investigation of marine unicellular bacteria, a new peptide, thalassospiramide G (1), along with thalassospiramides A and D (2–3), was discovered from a large culture of Thalassospira sp. The structure of thalassospiramide G, bearing γ-amino acids, such as 4-amino-5-hydroxy-penta-2-enoic acid (AHPEA), 4-amino-3,5-dihydroxy-pentanoic acid (ADPA), and unique 2-amino-1-(1H-indol-3-yl)ethanone (AIEN), was determined via extensive spectroscopic analysis. The absolute configuration of thalassospiramide D (3), including 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA), was rigorously determined by 1H–1H coupling constant analysis and chemical derivatization. Thalassospiramides A and D (2–3) inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated mouse macrophage RAW 264.7 cells, with IC50 values of 16.4 and 4.8 μM, respectively.
Collapse
Affiliation(s)
- Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Yuna Pyee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Korea; E-Mail:
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-2-880-2491; Fax: +82-2-762-8322
| |
Collapse
|
10
|
Jiménez T, Morcillo SP, Martín-Lasanta A, Collado-Sanz D, Cárdenas DJ, Gansäuer A, Justicia J, Cuerva JM. Combining the Power of TiIII-Mediated Processes for Easy Access to Hydroxylated Polycyclic Terpenoids: Synthesis of Sesterstatin 1 and C-D Rings of Aspergilloxide. Chemistry 2012; 18:12825-33. [DOI: 10.1002/chem.201201534] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Indexed: 12/30/2022]
|
11
|
Molinski TF, Reynolds KA, Morinaka BI. Symplocin A, a linear peptide from the Bahamian cyanobacterium Symploca sp. Configurational analysis of N,N-dimethylamino acids by chiral-phase HPLC of naphthacyl esters. JOURNAL OF NATURAL PRODUCTS 2012; 75:425-31. [PMID: 22360587 PMCID: PMC3694611 DOI: 10.1021/np200861n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The absolute stereostructures of the components of symplocin A (3), a new N,N-dimethyl-terminated peptide from the Bahamian cyanobacterium Symploca sp., were assigned from spectroscopic analysis, including MS, 2D NMR, and Marfey's analysis. The complete absolute configuration of symplocin A, including the unexpected D-configurations of the terminal N,N-dimethylisoleucine and valic acid residues, was assigned by chiral-phase HPLC of the corresponding 2-naphthacyl esters, a highly sensitive, complementary strategy for assignment of N-blocked peptide residues where Marfey's method is ineffectual or other methods fall short. Symplocin A exhibited potent activity as an inhibitor of cathepsin E (IC(50) 300 pM).
Collapse
Affiliation(s)
- Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States.
| | | | | |
Collapse
|