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Alcázar Magaña A, Vaswani A, Brown KS, Jiang Y, Alam MN, Caruso M, Lak P, Cheong P, Gray NE, Quinn JF, Soumyanath A, Stevens JF, Maier CS. Integrating High-Resolution Mass Spectral Data, Bioassays and Computational Models to Annotate Bioactives in Botanical Extracts: Case Study Analysis of C. asiatica Extract Associates Dicaffeoylquinic Acids with Protection against Amyloid-β Toxicity. Molecules 2024; 29:838. [PMID: 38398590 PMCID: PMC10892090 DOI: 10.3390/molecules29040838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Rapid screening of botanical extracts for the discovery of bioactive natural products was performed using a fractionation approach in conjunction with flow-injection high-resolution mass spectrometry for obtaining chemical fingerprints of each fraction, enabling the correlation of the relative abundance of molecular features (representing individual phytochemicals) with the read-outs of bioassays. We applied this strategy for discovering and identifying constituents of Centella asiatica (C. asiatica) that protect against Aβ cytotoxicity in vitro. C. asiatica has been associated with improving mental health and cognitive function, with potential use in Alzheimer's disease. Human neuroblastoma MC65 cells were exposed to subfractions of an aqueous extract of C. asiatica to evaluate the protective benefit derived from these subfractions against amyloid β-cytotoxicity. The % viability score of the cells exposed to each subfraction was used in conjunction with the intensity of the molecular features in two computational models, namely Elastic Net and selectivity ratio, to determine the relationship of the peak intensity of molecular features with % viability. Finally, the correlation of mass spectral features with MC65 protection and their abundance in different sub-fractions were visualized using GNPS molecular networking. Both computational methods unequivocally identified dicaffeoylquinic acids as providing strong protection against Aβ-toxicity in MC65 cells, in agreement with the protective effects observed for these compounds in previous preclinical model studies.
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Affiliation(s)
- Armando Alcázar Magaña
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (A.A.M.); (A.V.); (M.N.A.); (P.L.); (P.C.)
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR 97239, USA; (N.E.G.); (A.S.); (J.F.S.)
- Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ashish Vaswani
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (A.A.M.); (A.V.); (M.N.A.); (P.L.); (P.C.)
| | - Kevin S. Brown
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA;
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, 105 SW 26th Street, Corvallis, OR 97331, USA
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA;
| | - Md Nure Alam
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (A.A.M.); (A.V.); (M.N.A.); (P.L.); (P.C.)
| | - Maya Caruso
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA; (M.C.); (J.F.Q.)
| | - Parnian Lak
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (A.A.M.); (A.V.); (M.N.A.); (P.L.); (P.C.)
| | - Paul Cheong
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (A.A.M.); (A.V.); (M.N.A.); (P.L.); (P.C.)
| | - Nora E. Gray
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR 97239, USA; (N.E.G.); (A.S.); (J.F.S.)
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA; (M.C.); (J.F.Q.)
| | - Joseph F. Quinn
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA; (M.C.); (J.F.Q.)
- Parkinson’s Disease Research Education and Clinical Care Center, Veterans’ Administration Portland Health Care System, Portland, OR 97239, USA
| | - Amala Soumyanath
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR 97239, USA; (N.E.G.); (A.S.); (J.F.S.)
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA; (M.C.); (J.F.Q.)
| | - Jan F. Stevens
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR 97239, USA; (N.E.G.); (A.S.); (J.F.S.)
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA;
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Claudia S. Maier
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (A.A.M.); (A.V.); (M.N.A.); (P.L.); (P.C.)
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR 97239, USA; (N.E.G.); (A.S.); (J.F.S.)
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
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2
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Singh I, Seth A, Billesbølle CB, Braz J, Rodriguiz RM, Roy K, Bekele B, Craik V, Huang XP, Boytsov D, Pogorelov VM, Lak P, O'Donnell H, Sandtner W, Irwin JJ, Roth BL, Basbaum AI, Wetsel WC, Manglik A, Shoichet BK, Rudnick G. Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Cell 2023; 186:2160-2175.e17. [PMID: 37137306 PMCID: PMC10306110 DOI: 10.1016/j.cell.2023.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/05/2023] [Accepted: 04/06/2023] [Indexed: 05/05/2023]
Abstract
The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.
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Affiliation(s)
- Isha Singh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Anubha Seth
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Christian B Billesbølle
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Joao Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ramona M Rodriguiz
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Kasturi Roy
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Bethlehem Bekele
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xi-Ping Huang
- Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danila Boytsov
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Vladimir M Pogorelov
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Bryan L Roth
- Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - William C Wetsel
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA.
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA.
| | - Gary Rudnick
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA.
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3
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Dahlin JL, Hua BK, Zucconi BE, Nelson SD, Singh S, Carpenter AE, Shrimp JH, Lima-Fernandes E, Wawer MJ, Chung LPW, Agrawal A, O'Reilly M, Barsyte-Lovejoy D, Szewczyk M, Li F, Lak P, Cuellar M, Cole PA, Meier JL, Thomas T, Baell JB, Brown PJ, Walters MA, Clemons PA, Schreiber SL, Wagner BK. Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nat Commun 2023; 14:1364. [PMID: 36914634 PMCID: PMC10011410 DOI: 10.1038/s41467-023-36829-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Robust, generalizable approaches to identify compounds efficiently with undesirable mechanisms of action in complex cellular assays remain elusive. Such a process would be useful for hit triage during high-throughput screening and, ultimately, predictive toxicology during drug development. Here we generate cell painting and cellular health profiles for 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in a concentration-response format. A diversity of compounds that cause cellular damage produces bioactive cell painting morphologies, including cytoskeletal poisons, genotoxins, nonspecific electrophiles, and redox-active compounds. Further, we show that lower quality lysine acetyltransferase inhibitors and nonspecific electrophiles can be distinguished from more selective counterparts. We propose that the purposeful inclusion of cytotoxic and nuisance reference compounds such as those profiled in this resource will help with assay optimization and compound prioritization in complex cellular assays like cell painting.
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Grants
- R35 GM127045 NIGMS NIH HHS
- U01 CA272612 NCI NIH HHS
- T32 HL007627 NHLBI NIH HHS
- R37 GM062437 NIGMS NIH HHS
- S10 OD026839 NIH HHS
- R35 GM122481 NIGMS NIH HHS
- U01 DK123717 NIDDK NIH HHS
- Wellcome Trust
- R35 GM122547 NIGMS NIH HHS
- U01 CA217848 NCI NIH HHS
- K99 GM124357 NIGMS NIH HHS
- R35 GM149229 NIGMS NIH HHS
- This study was supported by the Ono Pharma Breakthrough Science Initiative Award (to BKW). Authors acknowledge the following financial support: JLD (NIH NHLBI, T32-HL007627); BKH (National Science Foundation, DGE1144152 and DGE1745303); BEZ (NIH NIGMS, K99-GM124357); SDN (Harvard University’s Graduate Prize Fellowship, Eli Lilly Graduate Fellowship in Chemistry); PA Cole (NIH NIGMS, R37-GM62437); SLS (NIGMS, R35-GM127045); BKW (Ono Pharma Foundation; NIH NIDDK, U01-DK123717); SS (NIH NIGMS, R35-GM122547). The authors gratefully acknowledge the use of the Opera Phenix High-Content/High-Throughput imaging system at the Broad Institute, funded by the NIH S10 grant OD026839. This research was supported in part by the Intramural/Extramural research program of the NCATS, NIH.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Beth E Zucconi
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Lawrence P W Chung
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Ayushi Agrawal
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | | | | | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Parnian Lak
- Department of Pharmaceutical Chemistry and Quantitative Biology Institute, University of California San Francisco, San Francisco, CA, USA
| | - Matthew Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Tim Thomas
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
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4
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Levit Kaplan A, Strachan RT, Braz JM, Craik V, Slocum S, Mangano T, Amabo V, O'Donnell H, Lak P, Basbaum AI, Roth BL, Shoichet BK. Structure-Based Design of a Chemical Probe Set for the 5-HT 5A Serotonin Receptor. J Med Chem 2022; 65:4201-4217. [PMID: 35195401 DOI: 10.1021/acs.jmedchem.1c02031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 5-HT5A receptor (5-HT5AR), for which no selective agonists and a few antagonists exist, remains the least understood serotonin receptor. A single commercial antagonist, SB-699551, has been widely used to investigate the 5-HT5AR function in neurological disorders, including pain, but this molecule has substantial liabilities as a chemical probe. Accordingly, we sought to develop an internally controlled probe set. Docking over 6 million molecules against a 5-HT5AR homology model identified 5 mid-μM ligands, one of which was optimized to UCSF678, a 42 nM arrestin-biased partial agonist at the 5-HT5AR with a more restricted off-target profile and decreased assay liabilities versus SB-699551. Site-directed mutagenesis supported the docked pose of UCSF678. Surprisingly, analogs of UCSF678 that lost the 5-HT5AR activity revealed that 5-HT5AR engagement is nonessential for alleviating pain, contrary to studies with less-selective ligands. UCSF678 and analogs constitute a selective probe set with which to study the function of the 5-HT5AR.
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Affiliation(s)
- Anat Levit Kaplan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Ryan T Strachan
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Joao M Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Samuel Slocum
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Thomas Mangano
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Vanessa Amabo
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States.,National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
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5
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Cabey K, Long DM, Law A, Gray NE, McClure C, Caruso M, Lak P, Wright KM, Stevens JF, Maier CS, Soumyanath A, Kretzschmar D. Withania somnifera and Centella asiatica Extracts Ameliorate Behavioral Deficits in an In Vivo Drosophila melanogaster Model of Oxidative Stress. Antioxidants (Basel) 2022; 11:antiox11010121. [PMID: 35052625 PMCID: PMC8773428 DOI: 10.3390/antiox11010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 12/31/2021] [Indexed: 02/05/2023] Open
Abstract
Due to an increase in the aging population, age-related diseases and age-related changes, such as diminished cognition and sleep disturbances, are an increasing health threat. It has been suggested that an increase in oxidative stress underlies many of these changes. Current treatments for these diseases and changes either have low efficacy or have deleterious side effects preventing long-time use. Therefore, alternative treatments that promote healthy aging and provide resilience against these health threats are needed. The herbs Withania somnifera and Centella asiatica may be two such alternatives because both have been connected with reducing oxidative stress and could therefore ameliorate age-related impairments. To test the effects of these herbs on behavioral phenotypes induced by oxidative stress, we used the Drosophila melanogaster sniffer mutant which has high levels of oxidative stress due to reduced carbonyl reductase activity. Effects on cognition and mobility were assessed using phototaxis assays and both, W. somnifera and C. asiatica water extracts improved phototaxis in sniffer mutants. In addition, W. somnifera improved nighttime sleep in male and female sniffer flies and promoted a less fragmented sleep pattern in male sniffer flies. This suggests that W. somnifera and C. asiatica can ameliorate oxidative stress-related changes in behavior and that by doing so they might promote healthy aging in humans.
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Affiliation(s)
- Kadine Cabey
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA;
- Helfgott Research Institute, National University of Natural Medicine, Portland, OR 97201, USA
| | - Dani M. Long
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR 97239, USA
| | - Alexander Law
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nora E. Gray
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Christine McClure
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Maya Caruso
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Parnian Lak
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (P.L.); (C.S.M.)
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA;
| | - Kirsten M. Wright
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Jan F. Stevens
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA;
- College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Claudia S. Maier
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA; (P.L.); (C.S.M.)
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA;
| | - Amala Soumyanath
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Department of Neurology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Doris Kretzschmar
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health and Science University, Portland, OR 97239, USA; (K.C.); (D.M.L.); (A.L.); (N.E.G.); (C.M.); (K.M.W.); (A.S.)
- Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR 97239, USA
- Correspondence:
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6
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Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proc Natl Acad Sci U S A 2021; 118:e2106195118. [PMID: 34475217 PMCID: PMC8433570 DOI: 10.1073/pnas.2106195118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Protein flexibility remains a major challenge in library docking because of difficulties in sampling conformational ensembles with accurate probabilities. Here, we use the model cavity site of T4 lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations: open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for the cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment; otherwise, high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm upshift and X-ray crystallography. From 33 selected molecules, we identified 18 ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability.
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Affiliation(s)
- Anna S Kamenik
- Institute of General, Inorganic, and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Isha Singh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Klaus R Liedl
- Institute of General, Inorganic, and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria;
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
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7
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Abstract
Small molecule colloidal aggregates adsorb and partially denature proteins, inhibiting them artifactually. Oddly, this inhibition is typically time-dependent. Two mechanisms might explain this: low concentrations of the colloid and enzyme might mean low encounter rates, or colloid-based protein denaturation might impose a kinetic barrier. These two mechanisms should have different concentration dependencies. Perplexingly, when enzyme concentration was increased, incubation times actually lengthened, inconsistent with both models and with classical chemical kinetics of solution species. We therefore considered molecular crowding, where colloids with lower protein surface density demand a shorter incubation time than more crowded colloids. To test this, we grew and shrank colloid surface area. As the surface area shrank, the incubation time lengthened, while as it increased, the converse was true. These observations support a crowding effect on protein binding to colloidal aggregates. Implications for drug delivery and for detecting aggregation-based inhibition will be discussed.
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Affiliation(s)
- Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Xuewen Du
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
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Paraiso IL, Revel JS, Choi J, Miranda CL, Lak P, Kioussi C, Bobe G, Gombart AF, Raber J, Maier CS, Stevens JF. Targeting the Liver-Brain Axis with Hop-Derived Flavonoids Improves Lipid Metabolism and Cognitive Performance in Mice. Mol Nutr Food Res 2020; 64:e2000341. [PMID: 32627931 PMCID: PMC8693899 DOI: 10.1002/mnfr.202000341] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/16/2020] [Indexed: 08/18/2023]
Abstract
SCOPE Sphingolipids including ceramides are implicated in the pathogenesis of obesity and insulin resistance. Correspondingly, inhibition of pro-inflammatory and neurotoxic ceramide accumulation prevents obesity-mediated insulin resistance and cognitive impairment. Increasing evidence suggests the farnesoid X receptor (FXR) is involved in ceramide metabolism, as bile acid-FXR crosstalk controls ceramide levels along the gut-liver axis. The authors previously reported that FXR agonist xanthohumol (XN), the principal prenylated flavonoid in hops (Humulus lupulus), and its hydrogenated derivatives, α,β-dihydroxanthohumol (DXN), and tetrahydroxanthohumol (TXN), ameliorated obesity-mediated insulin resistance, and cognitive impairment in mice fed a high-fat diet. METHODS AND RESULTS To better understand how the flavonoids improve both, lipid and bile acid profiles in the liver are analyzed, sphingolipid relative abundance in the hippocampus is measured, and linked them to metabolic and neurocognitive performance. XN, DXN, and TXN (30 mg kg-1 BW per day) decrease ceramide content in liver and hippocampus; the latter is linked to improvements in spatial learning and memory. In addition, XN, DXN, and TXN decrease hepatic cholesterol content by enhancing de novo synthesis of bile acids. CONCLUSION These observations suggest that XN, DXN, and TXN may alleviate obesity-induced metabolic and neurocognitive impairments by targeting the liver-brain axis.
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Affiliation(s)
- Ines L Paraiso
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Johana S Revel
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Jaewoo Choi
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
| | - Cristobal L Miranda
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Parnian Lak
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Chrissa Kioussi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Gerd Bobe
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Animal & Rangeland Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Adrian F Gombart
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Jacob Raber
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
- Department of Behavioral Neuroscience, Neurology, and Radiation Medicine, Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Jan F Stevens
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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Paraiso IL, Revel JS, Choi J, Miranda CL, Lak P, Kioussi C, Bobe G, Gombart AF, Raber J, Maier CS, Stevens JF. Front Cover: Targeting the Liver‐Brain Axis with Hop‐Derived Flavonoids Improves Lipid Metabolism and Cognitive Performance in Mice. Mol Nutr Food Res 2020. [DOI: 10.1002/mnfr.202070034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Zhu B, Luo R, Jin P, Li T, Oak HC, Giera S, Monk KR, Lak P, Shoichet BK, Piao X. GAIN domain-mediated cleavage is required for activation of G protein-coupled receptor 56 (GPR56) by its natural ligands and a small-molecule agonist. J Biol Chem 2019; 294:19246-19254. [PMID: 31628191 DOI: 10.1074/jbc.ra119.008234] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/02/2019] [Indexed: 12/15/2022] Open
Abstract
Adhesion G protein-coupled receptors (aGPCRs) represent a distinct family of GPCRs that regulate several developmental and physiological processes. Most aGPCRs undergo GPCR autoproteolysis-inducing domain-mediated protein cleavage, which produces a cryptic tethered agonist (termed Stachel (stinger)), and cleavage-dependent and -independent aGPCR signaling mechanisms have been described. aGPCR G1 (ADGRG1 or G protein-coupled receptor 56 (GPR56)) has pleiotropic functions in the development of multiple organ systems, which has broad implications for human diseases. To date, two natural GPR56 ligands, collagen III and tissue transglutaminase (TG2), and one small-molecule agonist, 3-α-acetoxydihydrodeoxygedunin (3-α-DOG), have been identified, in addition to a synthetic peptide, P19, that contains seven amino acids of the native Stachel sequence. However, the mechanisms by which these natural and small-molecule agonists signal through GPR56 remain unknown. Here we engineered a noncleavable receptor variant that retains signaling competence via the P19 peptide. We demonstrate that both natural and small-molecule agonists can activate only cleaved GPR56. Interestingly, TG2 required both receptor cleavage and the presence of a matrix protein, laminin, to activate GPR56, whereas collagen III and 3-α-DOG signaled without any cofactors. On the other hand, both TG2/laminin and collagen III activate the receptor by dissociating the N-terminal fragment from its C-terminal fragment, enabling activation by the Stachel sequence, whereas P19 and 3-α-DOG initiate downstream signaling without disengaging the N-terminal fragment from its C-terminal fragment. These findings deepen our understanding of how GPR56 signals via natural ligands, and a small-molecule agonist may be broadly applicable to other aGPCR family members.
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Affiliation(s)
- Beika Zhu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Weill Institute of Neuroscience, University of California, San Francisco, California 94143
| | - Rong Luo
- Department of Medicine, Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Peng Jin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Weill Institute of Neuroscience, University of California, San Francisco, California 94143
| | - Tao Li
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Weill Institute of Neuroscience, University of California, San Francisco, California 94143
| | - Hayeon C Oak
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Weill Institute of Neuroscience, University of California, San Francisco, California 94143
| | - Stefanie Giera
- Department of Medicine, Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Kelly R Monk
- Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239
| | - Parnian Lak
- Department of Pharmaceutical Chemistry and Quantitative Biology Institute, University of California, San Francisco, California 94143
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and Quantitative Biology Institute, University of California, San Francisco, California 94143
| | - Xianhua Piao
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Weill Institute of Neuroscience, University of California, San Francisco, California 94143 .,Department of Medicine, Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115.,Division of Neonatology, Department of Pediatrics, University of California, San Francisco, California 94158.,Newborn Brain Research Institute, University of California, San Francisco, California 94158
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11
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Jabbari Shiadeh SM, Pormohammad A, Hashemi A, Lak P. Global prevalence of antibiotic resistance in blood-isolated Enterococcus faecalis and Enterococcus faecium: a systematic review and meta-analysis. Infect Drug Resist 2019; 12:2713-2725. [PMID: 31564921 PMCID: PMC6731464 DOI: 10.2147/idr.s206084] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/08/2019] [Indexed: 01/08/2023] Open
Abstract
Introduction One of the global concerns is the increasing trend toward antimicrobial resistance and the consequent lack of efficient antimicrobials. Nosocomial infections present a big threat for patients all over the world and treatment with broad-spectrum antibiotics leads to outgrowth of hospital-associated resistant Enterococci clones that are very important in bloodstream infections. We surveyed the frequency and time trend of antibiotic resistance in Enterococci blood isolates from hospitalized patients in different regions of the world. Methods Literature from January 1, 2000 to May 20, 2018 was searched systematically using Medline (via PubMed), Embase, and Cochrane Library and all original publications on the antibiotic resistance prevalence in blood-isolated Enterococci strains with standard laboratory tests were included. Quality of the included studies was assessed with the modified Critical Appraisal Checklist recommended by the Joanna Briggs Institute. Depending on the heterogeneity test, we used either random or fixed effect models to assess the appropriateness of the pooled prevalence of drug resistance. Results A total of 291 studies were enrolled in the meta-analysis. Between all antibiotics, based on the WHO original offices, American countries showed the lowest prevalence of resistance for linezolid in Enterococcus faecalis. Regarding the prevalence of vancomycin resistance, Western Pacific, European, and American countries had the lowest level of resistance and South-East Asia and Eastern Mediterranean countries showed the highest level of resistance. Moreover, our findings for Enterococcus faecium indicated that America and South-East Asia had the lowest and the highest levels of resistance for linezolid, respectively. Conclusion Based on our findings, the prevalence of vancomycin-resistant E. faecium in bloodstream infections is significantly high, especially in Eastern Mediterranean countries, which is a massive warning signal for resistance to this broad-spectrum antibiotic. Therefore, the establishment of appropriate antibiotic usage guidelines should be essential in these countries.
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Affiliation(s)
| | - Ali Pormohammad
- Student Research Committee, Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parnian Lak
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
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12
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Donders EN, Ganesh AN, Torosyan H, Lak P, Shoichet BK, Shoichet MS. Triggered Release Enhances the Cytotoxicity of Stable Colloidal Drug Aggregates. ACS Chem Biol 2019; 14:1507-1514. [PMID: 31243955 DOI: 10.1021/acschembio.9b00247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemotherapeutics that self-assemble into colloids have limited efficacy above their critical aggregation concentration due to their inability to penetrate intact plasma membranes. Even when colloid uptake is promoted, issues with colloid escape from the endolysosomal pathway persist. By stabilizing acid-responsive lapatinib colloids through coaggregation with fulvestrant, and inclusion of transferrin, we demonstrate colloid internalization by cancer cells, where subsequent lapatinib ionization leads to endosomal leakage and increased cytotoxicity. These results demonstrate a strategy for triggered drug release from stable colloidal aggregates.
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Affiliation(s)
- Eric N. Donders
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Ahil N. Ganesh
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, Mail Box 2550, San Francisco, California 94143, United States
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, Mail Box 2550, San Francisco, California 94143, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, Mail Box 2550, San Francisco, California 94143, United States
| | - Molly S. Shoichet
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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13
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Charafeddine RA, Cortopassi WA, Lak P, Tan R, McKenney RJ, Jacobson MP, Barber DL, Wittmann T. Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH. J Biol Chem 2019; 294:8779-8790. [PMID: 30992364 DOI: 10.1074/jbc.ra118.007004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/13/2019] [Indexed: 12/20/2022] Open
Abstract
Tau, a member of the MAP2/tau family of microtubule-associated proteins, stabilizes and organizes axonal microtubules in healthy neurons. In neurodegenerative tauopathies, tau dissociates from microtubules and forms neurotoxic extracellular aggregates. MAP2/tau family proteins are characterized by three to five conserved, intrinsically disordered repeat regions that mediate electrostatic interactions with the microtubule surface. Here, we used molecular dynamics, microtubule-binding experiments, and live-cell microscopy, revealing that highly-conserved histidine residues near the C terminus of each microtubule-binding repeat are pH sensors that can modulate tau-microtubule interaction strength within the physiological intracellular pH range. We observed that at low pH (<7.5), these histidines are positively charged and interact with phenylalanine residues in a hydrophobic cleft between adjacent tubulin dimers. At higher pH (>7.5), tau deprotonation decreased binding to microtubules both in vitro and in cells. Electrostatic and hydrophobic characteristics of histidine were both required for tau-microtubule binding, as substitutions with constitutively and positively charged nonaromatic lysine or uncharged alanine greatly reduced or abolished tau-microtubule binding. Consistent with these findings, tau-microtubule binding was reduced in a cancer cell model with increased intracellular pH but was rapidly restored by decreasing the pH to normal levels. These results add detailed insights into the intracellular regulation of tau activity that may be relevant in both normal and pathological conditions.
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Affiliation(s)
- Rabab A Charafeddine
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143
| | - Wilian A Cortopassi
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Parnian Lak
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Ruensern Tan
- the Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Richard J McKenney
- the Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Matthew P Jacobson
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Diane L Barber
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143
| | - Torsten Wittmann
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143,
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Shiadeh SMJ, Hashemi A, Fallah F, Lak P, Azimi L, Rashidan M. First detection of efrAB, an ABC multidrug efflux pump in Enterococcus faecalis in Tehran, Iran. Acta Microbiol Immunol Hung 2019; 66:57-68. [PMID: 30246548 DOI: 10.1556/030.65.2018.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Enterococcus faecalis is one of the most significant pathogen in both nosocomial and community-acquired infections. Reduced susceptibility to antibiotics is in part due to efflux pumps. This study was conducted on 80 isolates of E. faecalis isolated from outpatients with urinary tract infection during a period of 1 year from April 2014 to April 2015. The antibiotic susceptibility patterns of isolates were determined by the disk diffusion method and presence of efrA and efrB genes was detected by PCR and sequencing. Minimum inhibitory concentrations (MICs) to ciprofloxacin (CIP) were measured with and without carbonyl cyanide 3-chlorophenylhydrazone (CCCP) by broth microdilution. The highest resistance rate was observed to erythromycin (83.3%) and the prevalence of efrA and efrB genes in all E. faecalis isolates was 100%. This study showed that 9 out of 13 (69.2%) ciprofloxacin-resistant isolates became less resistant at least fourfolds to CIP in the presence of efflux pump inhibitor. Our result showed that CCCP as an efflux inhibitor can increase effect of CIP as an efficient antibiotic and it is suggested that efrAB efflux pumps are involved in resistance to fluoroquinolone.
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Affiliation(s)
| | - Ali Hashemi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- 2 Pediatric Infections Research Center, Mofid Children’s Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parnian Lak
- 3 Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Leila Azimi
- 2 Pediatric Infections Research Center, Mofid Children’s Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Rashidan
- 4 School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
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Lak P. P2‐265: PREDICTION OF BRAIN AGING THROUGH ALTERATION OF TISSUE ELECTROMAGNETIC FIELDS. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Parnian Lak
- University of California San FranciscoSan FranciscoCAUSA
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16
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Gray NE, Alcazar Magana A, Lak P, Wright KM, Quinn J, Stevens JF, Maier CS, Soumyanath A. Centella asiatica - Phytochemistry and mechanisms of neuroprotection and cognitive enhancement. Phytochem Rev 2018; 17:161-194. [PMID: 31736679 PMCID: PMC6857646 DOI: 10.1007/s11101-017-9528-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 08/17/2017] [Indexed: 05/18/2023]
Abstract
This review describes in detail the phytochemistry and neurological effects of the medicinal herb Centella asiatica (L.) Urban. C. asiatica is a small perennial plant that grows in moist, tropical and sub-tropical regions throughout the world. Phytochemicals identified from C. asiatica to date include isoprenoids (sesquiterpenes, plant sterols, pentacyclic triterpenoids and saponins) and phenylpropanoid derivatives (eugenol derivatives, caffeoylquinic acids, and flavonoids). Contemporary methods for fingerprinting and characterization of compounds in C. asiatica extracts include liquid chromatography and/or ion mobility spectrometry in conjunction with high-resolution mass spectrometry. Multiple studies in rodent models, and a limited number of human studies support C. asiatica's traditional reputation as a cognitive enhancer, as well as its anxiolytic and anticonvulsant effects. Neuroprotective effects of C.asiatica are seen in several in vitro models, for example against beta amyloid toxicity, and appear to be associated with increased mitochondrial activity, improved antioxidant status, and/or inhibition of the pro-inflammatory enzyme, phospholipase A2. Neurotropic effects of C. asiatica include increased dendritic arborization and synaptogenesis, and may be due to modulations of signal transduction pathways such as ERK1/2 and Akt. Many of these neurotropic and neuroprotective properties of C.asiatica have been associated with the triterpene compounds asiatic acid, asiaticoside and madecassoside. More recently, caffeoylquinic acids are emerging as a second important group of active compounds in C. asiatica, with the potential of enhancing the Nrf2-antioxidant response pathway. The absorption, distribution, metabolism and excretion of the triterpenes, caffeoylquinic acids and flavonoids found in C. asiatica have been studied in humans and animal models, and the compounds or their metabolites found in the brain. This review highlights the remarkable potential for C. asiatica extracts and derivatives to be used in the treatment of neurological conditions, and considers the further research needed to actualize this possibility.
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Affiliation(s)
- Nora E. Gray
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| | | | - Parnian Lak
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331
| | - Kirsten M. Wright
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| | - Joseph Quinn
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
- Department of Neurology and Parkinson’s Disease Research Education and Clinical Care Center (PADRECC),
Portland Veterans Affairs Medical Center, Portland, OR, USA 97239
| | - Jan F. Stevens
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97331
| | - Claudia S. Maier
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97331
| | - Amala Soumyanath
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
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Lak P, Makeneni S, Woods RJ, Lowary TL. Specificity of furanoside-protein recognition through antibody engineering and molecular modeling. Chemistry 2014; 21:1138-48. [PMID: 25413161 DOI: 10.1002/chem.201405259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Indexed: 01/06/2023]
Abstract
Recognition of furanosides (five-membered ring sugars) by proteins plays important roles in host-pathogen interactions. In comparison to their six-membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in-depth molecular characterization of a furanoside-protein interaction system, between an antibody (CS-35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS-35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH-π interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries.
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Affiliation(s)
- Parnian Lak
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
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