1
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Rivera M, Ayon OS, Diaconescu-Grabari S, Pottel J, Moitessier N, Mittermaier A, McKeague M. A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states. Nucleic Acids Res 2024; 52:3164-3179. [PMID: 38375901 PMCID: PMC11014391 DOI: 10.1093/nar/gkae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
The capacity of riboswitches to undergo conformational changes in response to binding their native ligands is closely tied to their functional roles and is an attractive target for antimicrobial drug design. Here, we established a probe-based fluorescence anisotropy assay to monitor riboswitch conformational switching with high sensitivity and throughput. Using the Bacillus subtillis yitJ S-Box (SAM-I), Fusobacterium nucleatum impX RFN element of (FMN) and class-I cyclic-di-GMP from Vibrio cholerae riboswitches as model systems, we developed short fluorescent DNA probes that specifically recognize either ligand-free or -bound riboswitch conformational states. We showed that increasing concentrations of native ligands cause measurable and reproducible changes in fluorescence anisotropy that correlate with riboswitch conformational changes observed by native gel analysis. Furthermore, we applied our assay to several ligand analogues and confirmed that it can discriminate between ligands that bind, triggering the native conformational change, from those that bind without causing the conformational change. This new platform opens the possibility of high-throughput screening compound libraries to identify potential new antibiotics that specifically target functional conformational changes in riboswitches.
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Affiliation(s)
- Maira Rivera
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
| | - Omma S Ayon
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - Joshua Pottel
- Molecular Forecaster Inc. 910-2075 Robert Bourassa, Montreal, QC H3A 2L1, Canada
| | - Nicolas Moitessier
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
- Molecular Forecaster Inc. 910-2075 Robert Bourassa, Montreal, QC H3A 2L1, Canada
| | - Anthony Mittermaier
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
| | - Maureen McKeague
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 1Y6, Canada
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2
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Labarre A, Stille JK, Patrascu MB, Martins A, Pottel J, Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds─Challenges and Opportunities. J Chem Inf Model 2022; 62:1061-1077. [PMID: 35133156 DOI: 10.1021/acs.jcim.1c00701] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the years, structure-based design programs and specifically docking small molecules to proteins have become prominent in drug discovery. However, many of these computational tools have been developed to primarily dock enzyme inhibitors (and ligands to other protein classes) relying heavily on hydrogen bonds and electrostatic and hydrophobic interactions. In reality, many drug targets either feature metal ions, can be targeted covalently, or are simply not even proteins (e.g., nucleic acids). Herein, we describe several new features that we have implemented into Fitted to broaden its applicability to a wide range of covalent enzyme inhibitors and to metalloenzymes, where metal coordination is essential for drug binding. This updated version of our docking program was tested for its ability to predict the correct binding mode of drug-sized molecules in a large variety of proteins. We also report new datasets that were essential to demonstrate areas of success and those where additional efforts are required. This resource could be used by other program developers to assess their own software.
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Affiliation(s)
- Anne Labarre
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Julia K Stille
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Mihai Burai Patrascu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Andrew Martins
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Joshua Pottel
- Molecular Forecaster Inc., 7171, rue Frederick-Banting, Montreal H4S 1Z9, Quebec, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada.,Molecular Forecaster Inc., 7171, rue Frederick-Banting, Montreal H4S 1Z9, Quebec, Canada
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3
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Malone RW, Tisdall P, Fremont-Smith P, Liu Y, Huang XP, White KM, Miorin L, Moreno E, Alon A, Delaforge E, Hennecker CD, Wang G, Pottel J, Blair RV, Roy CJ, Smith N, Hall JM, Tomera KM, Shapiro G, Mittermaier A, Kruse AC, García-Sastre A, Roth BL, Glasspool-Malone J, Ricke DO. COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms. Front Pharmacol 2021; 12:633680. [PMID: 33833683 PMCID: PMC8021898 DOI: 10.3389/fphar.2021.633680] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 11/25/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. SARS-CoV-2 infection is necessary but not sufficient for development of clinical COVID-19 disease. Currently, there are no approved pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain obscure. We have investigated several plausible hypotheses for famotidine activity including antiviral and host-mediated mechanisms of action. We propose that the principal mechanism of action of famotidine for relieving COVID-19 symptoms involves on-target histamine receptor H2 activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. Based on these findings and associated hypothesis, new COVID-19 multi-drug treatment strategies based on repurposing well-characterized drugs are being developed and clinically tested, and many of these drugs are available worldwide in inexpensive generic oral forms suitable for both outpatient and inpatient treatment of COVID-19 disease.
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Affiliation(s)
- Robert W Malone
- RW Malone MD LLC, Madison, VA, United States.,Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, NY, United States
| | - Philip Tisdall
- Medical School Companion LLC, Marco Island, FL, United States
| | | | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Assaf Alon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Elise Delaforge
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | | | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | | | - Robert V Blair
- Tulane National Primate Research Center, Covington, LA, United Sates.,Department of Pathology and Laboratory Animal Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Chad J Roy
- Tulane National Primate Research Center, Covington, LA, United Sates.,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Nora Smith
- MIT Lincoln Laboratory, Lexington, MA, United States
| | - Julie M Hall
- Frank H. Netter MD School of Medicine - Quinnipiac University, Hamden, CT, United States
| | - Kevin M Tomera
- Department of Urology, Beloit Memorial Hospital, Beloit, WI, United States
| | | | | | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, NY, United States
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States
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4
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Malone RW, Tisdall P, Fremont-Smith P, Liu Y, Huang XP, White KM, Miorin L, Del Olmo EM, Alon A, Delaforge E, Hennecker CD, Wang G, Pottel J, Smith N, Hall JM, Shapiro G, Mittermaier A, Kruse AC, García-Sastre A, Roth BL, Glasspool-Malone J, Ricke DO. COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms. RESEARCH SQUARE 2020:rs.3.rs-30934. [PMID: 36575767 PMCID: PMC9793841 DOI: 10.21203/rs.3.rs-30934/v3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. Currently, there are no pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain obscure. We explore several plausible avenues of activity including antiviral and host-mediated actions. We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H 2 activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release.
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Affiliation(s)
| | | | | | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elena Moreno Del Olmo
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Assaf Alon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Elise Delaforge
- McGill University, Department of Chemistry, Montreal, Quebec, Canada
| | | | - Guanyu Wang
- McGill University, Department of Chemistry, Montreal, Quebec, Canada
| | | | | | - Julie M. Hall
- Frank H. Netter MD School of Medicine – Quinnipiac University, Hamden, CT
| | | | | | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC
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5
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Malone RW, Tisdall P, Fremont-Smith P, Liu Y, Huang XP, White KM, Miorin L, Del Olmo EM, Alon A, Delaforge E, Hennecker CD, Wang G, Pottel J, Smith N, Hall JM, Shapiro G, Mittermaier A, Kruse AC, García-Sastre A, Roth BL, Glasspool-Malone J, Ricke DO. COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms. Res Sq 2020:rs.3.rs-30934. [PMID: 32702719 PMCID: PMC7336703 DOI: 10.21203/rs.3.rs-30934/v2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. Currently, there are no pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain obscure. We explore several plausible avenues of activity including antiviral and host-mediated actions. We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H2 activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release.
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Affiliation(s)
| | | | | | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elena Moreno Del Olmo
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Assaf Alon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Elise Delaforge
- McGill University, Department of Chemistry, Montreal, Quebec, Canada
| | | | - Guanyu Wang
- McGill University, Department of Chemistry, Montreal, Quebec, Canada
| | | | | | - Julie M. Hall
- Frank H. Netter MD School of Medicine – Quinnipiac University, Hamden, CT
| | | | | | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC
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6
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Pottel J, Armstrong D, Zou L, Fekete A, Huang XP, Torosyan H, Bednarczyk D, Whitebread S, Bhhatarai B, Liang G, Jin H, Ghaemi SN, Slocum S, Lukacs KV, Irwin JJ, Berg EL, Giacomini KM, Roth BL, Shoichet BK, Urban L. The activities of drug inactive ingredients on biological targets. Science 2020; 369:403-413. [PMID: 32703874 DOI: 10.1126/science.aaz9906] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
Excipients, considered "inactive ingredients," are a major component of formulated drugs and play key roles in their pharmacokinetics. Despite their pervasiveness, whether they are active on any targets has not been systematically explored. We computed the likelihood that approved excipients would bind to molecular targets. Testing in vitro revealed 25 excipient activities, ranging from low-nanomolar to high-micromolar concentration. Another 109 activities were identified by testing against clinical safety targets. In cellular models, five excipients had fingerprints predictive of system-level toxicity. Exposures of seven excipients were investigated, and in certain populations, two of these may reach levels of in vitro target potency, including brain and gut exposure of thimerosal and its major metabolite, which had dopamine D3 receptor dissociation constant K d values of 320 and 210 nM, respectively. Although most excipients deserve their status as inert, many approved excipients may directly modulate physiologically relevant targets.
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Affiliation(s)
- Joshua Pottel
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Duncan Armstrong
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ling Zou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Alexander Fekete
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27759, USA
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Dallas Bednarczyk
- PK Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Steven Whitebread
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Barun Bhhatarai
- PK Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Guiqing Liang
- PK Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Hong Jin
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - S Nassir Ghaemi
- Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.,Tufts University School of Medicine, Boston, MA 02111, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Samuel Slocum
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27759, USA
| | - Katalin V Lukacs
- National Heart and Lung Institute, Imperial College, London SW7 2AZ, UK
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ellen L Berg
- Eurofins, DiscoverX, South San Francisco, CA 94080, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27759, USA
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Laszlo Urban
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
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7
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Burai Patrascu M, Pottel J, Pinus S, Bezanson M, Norrby PO, Moitessier N. From desktop to benchtop with automated computational workflows for computer-aided design in asymmetric catalysis. Nat Catal 2020. [DOI: 10.1038/s41929-020-0468-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Zou L, Spanogiannopoulos P, Pieper LM, Chien HC, Cai W, Khuri N, Pottel J, Vora B, Ni Z, Tsakalozou E, Zhang W, Shoichet BK, Giacomini KM, Turnbaugh PJ. Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives. Proc Natl Acad Sci U S A 2020; 117:16009-16018. [PMID: 32571913 PMCID: PMC7355017 DOI: 10.1073/pnas.1920483117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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] [Indexed: 12/14/2022] Open
Abstract
Food and drug products contain diverse and abundant small-molecule additives (excipients) with unclear impacts on human physiology, drug safety, and response. Here, we evaluate their potential impact on intestinal drug absorption. By screening 136 unique compounds for inhibition of the key intestinal transporter OATP2B1 we identified and validated 24 potent OATP2B1 inhibitors, characterized by higher molecular weight and hydrophobicity compared to poor or noninhibitors. OATP2B1 inhibitors were also enriched for dyes, including 8 azo (R-N=N-R') dyes. Pharmacokinetic studies in mice confirmed that FD&C Red No. 40, a common azo dye excipient and a potent inhibitor of OATP2B1, decreased the plasma level of the OATP2B1 substrate fexofenadine, suggesting that FD&C Red No. 40 has the potential to block drug absorption through OATP2B1 inhibition in vivo. However, the gut microbiomes of multiple unrelated healthy individuals as well as diverse human gut bacterial isolates were capable of inactivating the identified azo dye excipients, producing metabolites that no longer inhibit OATP2B1 transport. These results support a beneficial role for the microbiome in limiting the unintended effects of food and drug additives in the intestine and provide a framework for the data-driven selection of excipients. Furthermore, the ubiquity and genetic diversity of gut bacterial azoreductases coupled to experiments in conventionally raised and gnotobiotic mice suggest that variations in gut microbial community structure may be less important to consider relative to the high concentrations of azo dyes in food products, which have the potential to saturate gut bacterial enzymatic activity.
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Affiliation(s)
- Ling Zou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA 94143
| | - Lindsey M Pieper
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA 94143
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Natalia Khuri
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joshua Pottel
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- QB3 Institute, University of California, San Francisco, CA 94158
| | - Bianca Vora
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Zhanglin Ni
- Division of Quantitative Methods and Modeling, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993
| | - Eleftheria Tsakalozou
- Division of Quantitative Methods and Modeling, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- QB3 Institute, University of California, San Francisco, CA 94158
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA 94143;
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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9
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Zou L, Pottel J, Khuri N, Ngo HX, Ni Z, Tsakalozou E, Warren MS, Huang Y, Shoichet BK, Giacomini KM. Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP. Mol Pharm 2020; 17:748-756. [PMID: 31990564 DOI: 10.1021/acs.molpharmaceut.9b00658] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/15/2022]
Abstract
Mechanistic-understanding-based selection of excipients may improve formulation development strategies for generic drug products and potentially accelerate their approval. Our study aimed at investigating the effects of molecular excipients present in orally administered FDA-approved drug products on the intestinal efflux transporter, BCRP (ABCG2), which plays a critical role in drug absorption with potential implications on drug safety and efficacy. We determined the interactions of 136 oral molecular excipients with BCRP in isolated membrane vesicles and identified 26 excipients as BCRP inhibitors with IC50 values less than 5 μM using 3H-cholecystokinin octapeptide (3H-CCK8). These BCRP inhibitors belonged to three functional categories of excipients: dyes, surfactants, and flavoring agents. Compared with noninhibitors, BCRP inhibitors had significantly higher molecular weights and SLogP values. The inhibitory effects of excipients identified in membrane vesicles were also evaluated in BCRP-overexpressing HEK293 cells at similar concentrations. Only 1 of the 26 inhibitors of BCRP identified in vesicles inhibited BCRP-mediated 3H-oxypurinol uptake by more than 50%, consistent with the notion that BCRP inhibition depends on transmembrane or intracellular availability of the inhibitors. Collectively, the results of this study provide new information on excipient selection during the development of drug products with active pharmaceutical ingredients that are BCRP substrates.
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Affiliation(s)
- Ling Zou
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, California 94158, United States
| | - Joshua Pottel
- Department of Pharmaceutical Chemistry & QB3 Institute, University of California, San Francisco, California 94158, United States
| | - Natalia Khuri
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Huy X Ngo
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, California 94158, United States
| | - Zhanglin Ni
- Division of Quantitative Methods and Modeling, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Eleftheria Tsakalozou
- Division of Quantitative Methods and Modeling, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Mark S Warren
- Optivia Biotechnology, Inc., Santa Clara, California 95054, United States
| | - Yong Huang
- Optivia Biotechnology, Inc., Santa Clara, California 95054, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry & QB3 Institute, University of California, San Francisco, California 94158, United States
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, California 94158, United States
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10
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Abstract
Unrelated ligands, often found in drug discovery campaigns, can bind to the same receptor, even with the same protein residues. To investigate how this might occur, and whether it might be typically possible to find unrelated ligands for the same drug target, we sought examples of topologically unrelated ligands that bound to the same protein in the same site. Seventy-six pairs of ligands, each bound to the same protein (152 complexes total), were considered, classified into three groups. In the first (31 pairs of complexes), unrelated ligands interacted largely with the same pocket residues through different functional groups. In the second group (39 pairs), the unrelated ligand in each pair engaged different residues, though still within the same pocket. The smallest group (6 pairs) contained ligands with different scaffolds but with shared functional groups interacting with the same residues. We found that there are multiple chemically unrelated but physically similar functional groups that can complement any given local protein pocket; when these functional group substitutions are combined within a single molecule, they lead to topologically unrelated ligands that can each well-complement a site. It may be that many active and orthosteric sites can recognize topologically unrelated ligands.
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Affiliation(s)
- Joshua Pottel
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Anat Levit
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics & Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
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11
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Affiliation(s)
- Joshua Pottel
- Department of Chemistry, McGill University, 801
Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801
Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
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12
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Rocheleau S, Pottel J, Huskić I, Moitessier N. Highly Regioselective Monoacylation of Unprotected Glucopyranoside Using Transient Directing-Protecting Groups. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sylvain Rocheleau
- Department of Chemistry; McGill University; 801, Sherbrooke St·W. H3A 0B8 Montreal Canada
| | - Joshua Pottel
- Department of Chemistry; McGill University; 801, Sherbrooke St·W. H3A 0B8 Montreal Canada
| | - Igor Huskić
- Department of Chemistry; McGill University; 801, Sherbrooke St·W. H3A 0B8 Montreal Canada
| | - Nicolas Moitessier
- Department of Chemistry; McGill University; 801, Sherbrooke St·W. H3A 0B8 Montreal Canada
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13
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Irwin JJ, Pottel J, Zou L, Wen H, Zuk S, Zhang X, Sterling T, Shoichet BK, Lionberger R, Giacomini KM. A Molecular Basis for Innovation in Drug Excipients. Clin Pharmacol Ther 2016; 101:320-323. [PMID: 27557422 DOI: 10.1002/cpt.458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/12/2016] [Accepted: 08/14/2016] [Indexed: 12/27/2022]
Abstract
Excipients are ubiquitous in drug formulation, ensuring that active ingredient drugs are properly released on dosing, retain their properties over time, and are palatable, among other roles. Despite their crucial roles, surprisingly little is known about their systemic availability and activities on molecular targets. Here we review key excipient properties, introduce a public-accessible database that enumerates and categorizes them, and sketch a strategy for exploring their possible direct actions on molecular targets.
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Affiliation(s)
- J J Irwin
- Department of Pharmaceutical Chemistry & QB3 Institute, University of California, San Francisco, California, USA
| | - J Pottel
- Department of Pharmaceutical Chemistry & QB3 Institute, University of California, San Francisco, California, USA
| | - L Zou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - H Wen
- Food & Drug Administration, Silver Spring, Maryland, USA
| | - S Zuk
- Food & Drug Administration, Silver Spring, Maryland, USA
| | - X Zhang
- Food & Drug Administration, Silver Spring, Maryland, USA
| | - T Sterling
- Department of Pharmaceutical Chemistry & QB3 Institute, University of California, San Francisco, California, USA
| | - B K Shoichet
- Department of Pharmaceutical Chemistry & QB3 Institute, University of California, San Francisco, California, USA
| | - R Lionberger
- Food & Drug Administration, Silver Spring, Maryland, USA
| | - K M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
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14
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Moitessier N, Pottel J, Therrien E, Englebienne P, Liu Z, Tomberg A, Corbeil CR. Medicinal Chemistry Projects Requiring Imaginative Structure-Based Drug Design Methods. Acc Chem Res 2016; 49:1646-57. [PMID: 27529781 DOI: 10.1021/acs.accounts.6b00185] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Computational methods for docking small molecules to proteins are prominent in drug discovery. There are hundreds, if not thousands, of documented examples-and several pertinent cases within our research program. Fifteen years ago, our first docking-guided drug design project yielded nanomolar metalloproteinase inhibitors and illustrated the potential of structure-based drug design. Subsequent applications of docking programs to the design of integrin antagonists, BACE-1 inhibitors, and aminoglycosides binding to bacterial RNA demonstrated that available docking programs needed significant improvement. At that time, docking programs primarily considered flexible ligands and rigid proteins. We demonstrated that accounting for protein flexibility, employing displaceable water molecules, and using ligand-based pharmacophores improved the docking accuracy of existing methods-enabling the design of bioactive molecules. The success prompted the development of our own program, Fitted, implementing all of these aspects. The primary motivation has always been to respond to the needs of drug design studies; the majority of the concepts behind the evolution of Fitted are rooted in medicinal chemistry projects and collaborations. Several examples follow: (1) Searching for HDAC inhibitors led us to develop methods considering drug-zinc coordination and its effect on the pKa of surrounding residues. (2) Targeting covalent prolyl oligopeptidase (POP) inhibitors prompted an update to Fitted to identify reactive groups and form bonds with a given residue (e.g., a catalytic residue) when the geometry allows it. Fitted-the first fully automated covalent docking program-was successfully applied to the discovery of four new classes of covalent POP inhibitors. As a result, efficient stereoselective syntheses of a few screening hits were prioritized rather than synthesizing large chemical libraries-yielding nanomolar inhibitors. (3) In order to study the metabolism of POP inhibitors by cytochrome P450 enzymes (CYPs)-for toxicology studies-the program Impacts was derived from Fitted and helped us to reveal a complex metabolism with unforeseen stereocenter isomerizations. These efforts, combined with those of other docking software developers, have strengthened our understanding of the complex drug-protein binding process while providing the medicinal chemistry community with useful tools that have led to drug discoveries. In this Account, we describe our contributions over the past 15 years-within their historical context-to the design of drug candidates, including BACE-1 inhibitors, POP covalent inhibitors, G-quadruplex binders, and aminoglycosides binding to nucleic acids. We also remark the necessary developments of docking programs, specifically Fitted, that enabled structure-based design to flourish and yielded multiple fruitful, rational medicinal chemistry campaigns.
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Affiliation(s)
- Nicolas Moitessier
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Joshua Pottel
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Eric Therrien
- Molecular Forecaster Inc., 969
Marc-Aurèle-Fortin, Laval, Québec, Canada H7L 6H9
| | - Pablo Englebienne
- Royal HaskoningDHV, Laan 1914
35, 3818 EX Amersfoort, The Netherlands
| | - Zhaomin Liu
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Anna Tomberg
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Christopher R. Corbeil
- Human
Health Therapeutics, National Research Council Canada, 6100 Royalmount
Avenue, Montréal, Québec, Canada H4P 2R2
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15
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Liu Z, Pottel J, Shahamat M, Tomberg A, Labute P, Moitessier N. Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner. J Chem Inf Model 2016; 56:788-801. [DOI: 10.1021/acs.jcim.6b00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Zhaomin Liu
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8
| | - Joshua Pottel
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8
| | - Moeed Shahamat
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8
| | - Anna Tomberg
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc., 1010 Sherbrooke St. W., Montréal, QC, Canada H3A 2R7
| | - Nicolas Moitessier
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8
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16
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Abstract
Protein engineers have long been hard at work to harness biocatalysts as a natural source of regio-, stereo-, and chemoselectivity in order to carry out chemistry (reactions and/or substrates) not previously achieved with these enzymes. The extreme labor demands and exponential number of mutation combinations have induced computational advances in this domain. The first step in our virtual approach is to predict the correct conformations upon mutation of residues (i.e., rebuilding side chains). For this purpose, we opted for a combination of molecular mechanics and statistical data. In this work, we have developed automated computational tools to extract protein structural information and created conformational libraries for each amino acid dependent on a variable number of parameters (e.g., resolution, flexibility, secondary structure). We have also developed the necessary tool to apply the mutation and optimize the conformation accordingly. For side-chain conformation prediction, we obtained overall average root-mean-square deviations (RMSDs) of 0.91 and 1.01 Å for the 18 flexible natural amino acids within two distinct sets of over 3000 and 1500 side-chain residues, respectively. The commonly used dihedral angle differences were also evaluated and performed worse than the state of the art. These two metrics are also compared. Furthermore, we generated a family-specific library for kinases that produced an average 2% lower RMSD upon side-chain reconstruction and a residue-specific library that yielded a 17% improvement. Ultimately, since our protein engineering outlook involves using our docking software, Fitted/Impacts, we applied our mutation protocol to a benchmarked data set for self- and cross-docking. Our side-chain reconstruction does not hinder our docking software, demonstrating differences in pose prediction accuracy of approximately 2% (RMSD cutoff metric) for a set of over 200 protein/ligand structures. Similarly, when docking to a set of over 100 kinases, side-chain reconstruction (using both general and biased conformation libraries) had minimal detriment to the docking accuracy.
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Affiliation(s)
- Joshua Pottel
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
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17
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Mendoza-Sanchez R, Cotnoir-White D, Kulpa J, Jutras I, Pottel J, Moitessier N, Mader S, Gleason JL. Design, synthesis and evaluation of antiestrogen and histone deacetylase inhibitor molecular hybrids. Bioorg Med Chem 2015; 23:7597-606. [DOI: 10.1016/j.bmc.2015.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 01/28/2023]
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18
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Tomberg A, Pottel J, Liu Z, Labute P, Moitessier N. Understanding P450-mediated Bio-transformations into Epoxide and Phenolic Metabolites. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Tomberg A, Pottel J, Liu Z, Labute P, Moitessier N. Understanding P450-mediated Bio-transformations into Epoxide and Phenolic Metabolites. Angew Chem Int Ed Engl 2015; 54:13743-7. [PMID: 26418278 DOI: 10.1002/anie.201506131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 07/03/2015] [Revised: 09/10/2015] [Indexed: 11/06/2022]
Abstract
Adverse drug reactions are commonly the result of cytochrome P450 enzymes (CYPs) converting the drugs into reactive metabolites. Thus, information about the CYP bioactivation of drugs would not only provide insight into metabolic stability, but also into the potential toxicity. For example, oxidation of phenyl rings may lead to either toxic epoxides or safer phenols. Herein, we demonstrate that the potential to form reactive metabolites is encoded primarily in the properties of the molecule to be oxidized. While the enzyme positions the molecule inside the binding pocket (selects the site of metabolism), the subsequent reaction is only dependent on the substrate itself. To test this hypothesis, we used this observation as a predictor of drug inherent toxicity. This approach was used to successfully identify the formation of reactive metabolites in over 100 drug molecules. These results provide a new perspective on the impact of functional groups on aromatic oxidation of drugs and their effects on toxicity.
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Affiliation(s)
- Anna Tomberg
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8 (Canada)
| | - Joshua Pottel
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8 (Canada)
| | - Zhaomin Liu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8 (Canada)
| | - Paul Labute
- Chemical Computing Group Inc., 1010 Sherbrooke Street West, Montreal, QC, H3A 2R7 (Canada)
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8 (Canada).
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20
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Schiavini P, Pottel J, Moitessier N, Auclair K. Back Cover: Metabolic Instability of Cyanothiazolidine-Based Prolyl Oligopeptidase Inhibitors: a Structural Assignment Challenge and Potential Medicinal Chemistry Implications (ChemMedChem 7/2015). ChemMedChem 2015. [DOI: 10.1002/cmdc.201590022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Schiavini P, Pottel J, Moitessier N, Auclair K. Metabolic Instability of Cyanothiazolidine-Based Prolyl Oligopeptidase Inhibitors: a Structural Assignment Challenge and Potential Medicinal Chemistry Implications. ChemMedChem 2015; 10:1174-83. [PMID: 26018317 DOI: 10.1002/cmdc.201500114] [Citation(s) in RCA: 8] [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: 03/11/2015] [Indexed: 11/07/2022]
Abstract
As part of the development of cyanothiazolidine-based prolyl oligopeptidase inhibitors, initial metabolism studies suggested multiple sites of oxidation by P450 enzymes. Surprisingly, in-depth investigations revealed that epimerization at multiple stereogenic centers was responsible for the conversion of the single primary metabolite into a panel of secondary metabolites. The rapid isomerization of all seven detected molecules precluded the use of NMR spectroscopy or X-ray crystallography for complete structural determination, presenting an interesting structure elucidation challenge. Through a combination of LC-MS analysis, synthetic work, deuterium exchange studies, and computational predictions, we were able to characterize all metabolites and to elucidate their dynamic behavior in solution. In the context of drug development, this study reveals that cyanothiazolidine moieties are problematic due to their rapid P450-mediated oxidation and the unpredictable stability of the corresponding metabolites.
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Affiliation(s)
- Paolo Schiavini
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8 (Canada)
| | - Joshua Pottel
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8 (Canada)
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8 (Canada).
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8 (Canada).
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22
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Pottel J, Therrien E, Gleason JL, Moitessier N. Docking ligands into flexible and solvated macromolecules. 6. Development and application to the docking of HDACs and other zinc metalloenzymes inhibitors. J Chem Inf Model 2014; 54:254-65. [PMID: 24364808 DOI: 10.1021/ci400550m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Metalloenzymes are ubiquitous proteins which feature one or more metal ions either directly involved in the enzymatic activity and/or structural properties (i.e., zinc fingers). Several members of this class take advantage of the Lewis acidic properties of zinc ions to carry out their various catalytic transformations including isomerization or amide cleavage. These enzymes have been validated as drug targets for a number of diseases including cancer; however, despite their pharmaceutical relevance and the availability of crystal structures, structure-based drug design methods have been poorly and indirectly parametrized for these classes of enzymes. More specifically, the metal coordination component and proton transfers of the process of drugs binding to metalloenzymes have been inadequately modeled by current docking programs, if at all. In addition, several known issues, such as coordination geometry, atomic charge variability, and a potential proton transfer from small molecules to a neighboring basic residue, have often been ignored. We report herein the development of specific functions and parameters to account for zinc-drug coordination focusing on the above-listed phenomena and their impact on docking to zinc metalloenzymes. These atom-type-dependent but atomic charge-independent functions implemented into Fitted 3.1 enable the simulation of drug binding to metalloenzymes, considering an acid-base reaction with a neighboring residue when necessary with good accuracy.
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Affiliation(s)
- Joshua Pottel
- Department of Chemistry, McGill University , 801 Sherbrooke St W, Montreal, QC, Canada H3A 0B8
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23
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Bezanson M, Pottel J, Bilbeisi R, Toumieux S, Cueto M, Moitessier N. Stereo- and Regioselective Synthesis of Polysubstituted Chiral 1,4-Oxazepanes. J Org Chem 2013; 78:872-85. [PMID: 23305339 DOI: 10.1021/jo3021715] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Michelle Bezanson
- Department of Chemistry, McGill University, 801 Sherbrooke Street
West, Montreal, Québec, Canada H3A 2K6
| | - Joshua Pottel
- Department of Chemistry, McGill University, 801 Sherbrooke Street
West, Montreal, Québec, Canada H3A 2K6
| | - Rana Bilbeisi
- Department of Chemistry, McGill University, 801 Sherbrooke Street
West, Montreal, Québec, Canada H3A 2K6
| | - Sylvestre Toumieux
- Department of Chemistry, McGill University, 801 Sherbrooke Street
West, Montreal, Québec, Canada H3A 2K6
| | - Mickaël Cueto
- Department of Chemistry, McGill University, 801 Sherbrooke Street
West, Montreal, Québec, Canada H3A 2K6
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street
West, Montreal, Québec, Canada H3A 2K6
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24
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Campagna-Slater V, Pottel J, Therrien E, Cantin LD, Moitessier N. Development of a computational tool to rival experts in the prediction of sites of metabolism of xenobiotics by p450s. J Chem Inf Model 2012; 52:2471-83. [PMID: 22916680 DOI: 10.1021/ci3003073] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The metabolism of xenobiotics--and more specifically drugs--in the liver is a critical process controlling their half-life. Although there exist experimental methods, which measure the metabolic stability of xenobiotics and identify their metabolites, developing higher throughput predictive methods is an avenue of research. It is expected that predicting the chemical nature of the metabolites would be an asset for designing safer drugs and/or drugs with modulated half-lives. We have developed IMPACTS (In-silico Metabolism Prediction by Activated Cytochromes and Transition States), a computational tool combining docking to metabolic enzymes, transition state modeling, and rule-based substrate reactivity prediction to predict the site of metabolism (SoM) of xenobiotics. Its application to sets of CYP1A2, CYP2C9, CYP2D6, and CYP3A4 substrates and comparison to experts' predictions demonstrates its accuracy and significance. IMPACTS identified an experimentally observed SoM in the top 2 predicted sites for 77% of the substrates, while the accuracy of biotransformation experts' prediction was 65%. Application of IMPACTS to external sets and comparison of its accuracy to those of eleven other methods further validated the method implemented in IMPACTS.
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Affiliation(s)
- Valérie Campagna-Slater
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC H3A 0B8, Canada
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