1
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Nawa F, Sai M, Vietor J, Schwarzenbach R, Bitić A, Wolff S, Ildefeld N, Pabel J, Wein T, Marschner JA, Heering J, Merk D. Tuning RXR Modulators for PGC1α Recruitment. J Med Chem 2024; 67:16338-16354. [PMID: 39258574 DOI: 10.1021/acs.jmedchem.4c01231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
The molecular activation mechanism of the nuclear retinoid X receptors (RXRs) crucially involves ligand-induced corepressor release and coactivator recruitment which mediate transcriptional repression or activation. The ability of RXR to bind diverse coactivators suggests that a coregulator-selective modulation by ligands may open an avenue to tissue- or gene-selective RXR activation. Here, we identified strong induction of peroxisome proliferator-activated receptor γ coactivator 1α (PGC1α) binding to RXR by a synthetic agonist but not by the endogenous ligand 9-cis retinoic acid. Structure-guided diversification of this lead resulted in a set of three structurally related RXR agonists with different ability to promote PGC1α recruitment in cell-free and cellular context. These results demonstrate that selective modulation of coregulator recruitment to RXR can be achieved with molecular glues and potentially open new therapeutic opportunities by targeting the ligand-induced RXR-PGC1α interaction.
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Affiliation(s)
- Felix Nawa
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Minh Sai
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Jan Vietor
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Roman Schwarzenbach
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Anesa Bitić
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Sina Wolff
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Niklas Ildefeld
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jörg Pabel
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Thomas Wein
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596 Frankfurt, Germany
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
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2
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Andrade C, Sousa BKDP, Sigurdardóttir S, Bourgard C, Borba J, Clementino L, Salazar-Alvarez LC, Groustra S, Zigweid R, Khim M, Staker B, Costa F, Eriksson L, Sunnerhagen P. Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase. RESEARCH SQUARE 2024:rs.3.rs-3963523. [PMID: 38463971 PMCID: PMC10925453 DOI: 10.21203/rs.3.rs-3963523/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Malaria remains a significant public health challenge, with Plasmodium vivax being the species responsible for the most prevalent form of the disease. Given the limited therapeutic options available, the search for new antimalarials against P. vivax is urgent. This study aims to identify new inhibitors for P. vivax N-myristoyltransferase (PvNMT), an essential drug target against malaria. Through a validated virtual screening campaign, we prioritized 23 candidates for further testing. In the yeast NMT system, seven compounds exhibit a potential inhibitor phenotype. In vitro antimalarial phenotypic assays confirmed the activity of four candidates while demonstrating an absence of cytotoxicity. Enzymatic assays reveal LabMol-394 as the most promising inhibitor, displaying selectivity against the parasite and a strong correlation within the yeast system. Furthermore, molecular dynamics simulations shed some light into its binding mode. This study constitutes a substantial contribution to the exploration of a selective quinoline scaffold and provides valuable insights into the development of new antimalarial candidates.
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3
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Acin‐Perez R, Benincá C, Fernandez del Rio L, Shu C, Baghdasarian S, Zanette V, Gerle C, Jiko C, Khairallah R, Khan S, Rincon Fernandez Pacheco D, Shabane B, Erion K, Masand R, Dugar S, Ghenoiu C, Schreiner G, Stiles L, Liesa M, Shirihai OS. Inhibition of ATP synthase reverse activity restores energy homeostasis in mitochondrial pathologies. EMBO J 2023; 42:e111699. [PMID: 36912136 PMCID: PMC10183817 DOI: 10.15252/embj.2022111699] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 03/14/2023] Open
Abstract
The maintenance of cellular function relies on the close regulation of adenosine triphosphate (ATP) synthesis and hydrolysis. ATP hydrolysis by mitochondrial ATP Synthase (CV) is induced by loss of proton motive force and inhibited by the mitochondrial protein ATPase inhibitor (ATPIF1). The extent of CV hydrolytic activity and its impact on cellular energetics remains unknown due to the lack of selective hydrolysis inhibitors of CV. We find that CV hydrolytic activity takes place in coupled intact mitochondria and is increased by respiratory chain defects. We identified (+)-Epicatechin as a selective inhibitor of ATP hydrolysis that binds CV while preventing the binding of ATPIF1. In cells with Complex-III deficiency, we show that inhibition of CV hydrolytic activity by (+)-Epichatechin is sufficient to restore ATP content without restoring respiratory function. Inhibition of CV-ATP hydrolysis in a mouse model of Duchenne Muscular Dystrophy is sufficient to improve muscle force without any increase in mitochondrial content. We conclude that the impact of compromised mitochondrial respiration can be lessened using hydrolysis-selective inhibitors of CV.
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Affiliation(s)
- Rebeca Acin‐Perez
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Cristiane Benincá
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Lucia Fernandez del Rio
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Cynthia Shu
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Siyouneh Baghdasarian
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Vanessa Zanette
- Department of BioinformaticsUniversity Federal of ParanaCuritibaBrazil
| | - Christoph Gerle
- Institute for Protein ResearchOsaka UniversitySuitaJapan
- RIKEN SPring‐8 CenterSayo‐gunJapan
| | - Chimari Jiko
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversityKyotoJapan
| | | | | | | | - Byourak Shabane
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | | | | | | | | | | | - Linsey Stiles
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of Molecular and Medical PharmacologyUniversity of CaliforniaLos AngelesCAUSA
| | - Marc Liesa
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of Molecular and Medical PharmacologyUniversity of CaliforniaLos AngelesCAUSA
- Molecular Cellular Integrative PhysiologyUniversity of CaliforniaLos AngelesCAUSA
- Institut de Biologia Molecular de Barcelona, IBMB, CSICBarcelonaCataloniaSpain
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of Molecular and Medical PharmacologyUniversity of CaliforniaLos AngelesCAUSA
- Molecular Cellular Integrative PhysiologyUniversity of CaliforniaLos AngelesCAUSA
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4
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Díaz-Rovira AM, Martín H, Beuming T, Díaz L, Guallar V, Ray SS. Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. J Chem Inf Model 2023; 63:1668-1674. [PMID: 36892986 DOI: 10.1021/acs.jcim.2c01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Machine learning-based protein structure prediction algorithms, such as RosettaFold and AlphaFold2, have greatly impacted the structural biology field, arousing a fair amount of discussion around their potential role in drug discovery. While there are few preliminary studies addressing the usage of these models in virtual screening, none of them focus on the prospect of hit-finding in a real-world virtual screen with a model based on low prior structural information. In order to address this, we have developed an AlphaFold2 version where we exclude all structural templates with more than 30% sequence identity from the model-building process. In a previous study, we used those models in conjunction with state-of-the-art free energy perturbation methods and demonstrated that it is possible to obtain quantitatively accurate results. In this work, we focus on using these structures in rigid receptor-ligand docking studies. Our results indicate that using out-of-the-box Alphafold2 models is not an ideal scenario for virtual screening campaigns; in fact, we strongly recommend to include some post-processing modeling to drive the binding site into a more realistic holo model.
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Affiliation(s)
- Anna M Díaz-Rovira
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | | | - Thijs Beuming
- Latham Biopharm Group, 101 Main Street, Suite 1400, Cambridge, Massachusetts 02142, United States
| | - Lucía Díaz
- Nostrum Biodiscovery S.L., E-08029 Barcelona, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain.,Nostrum Biodiscovery S.L., E-08029 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Soumya S Ray
- RA Capital, 200 Berkeley Street, Boston, Massachusetts 02116, United States.,3-Dimensional Consulting, 134 Franklin Avenue, Quincy, Massachusetts 02170, United States
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5
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Beuming T, Martín H, Díaz-Rovira AM, Díaz L, Guallar V, Ray SS. Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures. J Chem Inf Model 2022; 62:4351-4360. [PMID: 36099477 DOI: 10.1021/acs.jcim.2c00796] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The availability of AlphaFold2 has led to great excitement in the scientific community─particularly among drug hunters─due to the ability of the algorithm to predict protein structures with high accuracy. However, beyond globally accurate protein structure prediction, it remains to be determined whether ligand binding sites are predicted with sufficient accuracy in these structures to be useful in supporting computationally driven drug discovery programs. We explored this question by performing free-energy perturbation (FEP) calculations on a set of well-studied protein-ligand complexes, where AlphaFold2 predictions were performed by removing all templates with >30% identity to the target protein from the training set. We observed that in most cases, the ΔΔG values for ligand transformations calculated with FEP, using these prospective AlphaFold2 structures, were comparable in accuracy to the corresponding calculations previously carried out using crystal structures. We conclude that under the right circumstances, AlphaFold2-modeled structures are accurate enough to be used by physics-based methods such as FEP in typical lead optimization stages of a drug discovery program.
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Affiliation(s)
- Thijs Beuming
- Latham Biopharm Group, 101 Main Street, Suite 1400, Cambridge, Massachusetts 02142, United States
| | | | - Anna M Díaz-Rovira
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Lucía Díaz
- NOSTRUM BIODISCOVERY S.L., E-08029 Barcelona, Spain
| | - Victor Guallar
- NOSTRUM BIODISCOVERY S.L., E-08029 Barcelona, Spain.,Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Soumya S Ray
- RA Capital, 200 Berkeley Street, Boston Massachusetts 02116, United States
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6
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis. Nat Commun 2020; 11:3216. [PMID: 32587248 PMCID: PMC7316778 DOI: 10.1038/s41467-020-17027-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine residue into cysteine at the DFG-1 position in the ATP-binding pocket, we sensitize the non-receptor tyrosine kinase FES towards covalent labeling by a complementary fluorescent chemical probe. This mutation is introduced in the endogenous FES gene of HL-60 cells using CRISPR/Cas9 gene editing. Leveraging the temporal and acute control offered by our strategy, we show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis via SYK kinase activation. This chemical genetics strategy holds promise as a target validation method for kinases.
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8
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Nešić D, Zhang Y, Spasic A, Li J, Provasi D, Filizola M, Walz T, Coller BS. Cryo-Electron Microscopy Structure of the αIIbβ3-Abciximab Complex. Arterioscler Thromb Vasc Biol 2020; 40:624-637. [PMID: 31969014 PMCID: PMC7047619 DOI: 10.1161/atvbaha.119.313671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/30/2019] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The αIIbβ3 antagonist antiplatelet drug abciximab is the chimeric antigen-binding fragment comprising the variable regions of murine monoclonal antibody 7E3 and the constant domains of human IgG1 and light chain κ. Previous mutagenesis studies suggested that abciximab binds to the β3 C177-C184 specificity-determining loop (SDL) and Trp129 on the adjacent β1-α1 helix. These studies could not, however, assess whether 7E3 or abciximab prevents fibrinogen binding by steric interference, disruption of either the αIIbβ3-binding pocket for fibrinogen or the β3 SDL (which is not part of the binding pocket but affects fibrinogen binding), or some combination of these effects. To address this gap, we used cryo-electron microscopy to determine the structure of the αIIbβ3-abciximab complex at 2.8 Å resolution. Approach and Results: The interacting surface of abciximab is comprised of residues from all 3 complementarity-determining regions of both the light and heavy chains, with high representation of aromatic residues. Binding is primarily to the β3 SDL and neighboring residues, the β1-α1 helix, and β3 residues Ser211, Val212 and Met335. Unexpectedly, the structure also indicated several interactions with αIIb. As judged by the cryo-electron microscopy model, molecular-dynamics simulations, and mutagenesis, the binding of abciximab does not appear to rely on the interaction with the αIIb residues and does not result in disruption of the fibrinogen-binding pocket; it does, however, compress and reduce the flexibility of the SDL. CONCLUSIONS We deduce that abciximab prevents ligand binding by steric interference, with a potential contribution via displacement of the SDL and limitation of the flexibility of the SDL residues.
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Affiliation(s)
- Dragana Nešić
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, Rockefeller University, New York, NY
| | - Yixiao Zhang
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY
| | - Aleksandar Spasic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jihong Li
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, Rockefeller University, New York, NY
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY
| | - Barry S. Coller
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, Rockefeller University, New York, NY
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9
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Cappel D, Jerome S, Hessler G, Matter H. Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations. J Chem Inf Model 2020; 60:1432-1444. [DOI: 10.1021/acs.jcim.9b01118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Steven Jerome
- Schrödinger Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Gerhard Hessler
- Integrated Drug Discovery (IDD), Synthetic Molecular Design, Sanofi-Aventis Deutschland GmbH, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Hans Matter
- Integrated Drug Discovery (IDD), Synthetic Molecular Design, Sanofi-Aventis Deutschland GmbH, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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10
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Atomistic simulations shed new light on the activation mechanisms of RORγ and classify it as Type III nuclear hormone receptor regarding ligand-binding paths. Sci Rep 2019; 9:17249. [PMID: 31754232 PMCID: PMC6872664 DOI: 10.1038/s41598-019-52319-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/11/2019] [Indexed: 12/18/2022] Open
Abstract
The molecular recognition of the RORγ nuclear hormone receptor (NHR) ligand-binding domain (LBD) has been extensively studied with numerous X-ray crystal structures. However, the picture afforded by these complexes is static and does not fully explain the functional behavior of the LBD. In particular, the apo structure of the LBD seems to be in a fully active state, with no obvious differences to the agonist-bound structure. Further, several atypical in vivo inverse agonists have surprisingly been found to co-crystallize with the LBD in agonist mode (with co-activator), leading to a disconnection between molecular recognition and functional activity. Moreover, the experimental structures give no clues on how RORγ LBD binders access the interior of the LBD. To address all these points, we probe here, with a variety of simulation techniques, the fine structural balance of the RORγ LBD in its apo vs. holo form, the differences in flexibility and stability of the LBD in complex with agonists vs. inverse agonists and how binders diffuse in and out of the LBD in unbiased simulations. Our data conclusively point to the stability afforded by the so-called “agonist lock” between H479 and Y502 and the precise location of Helix 12 (H12) for the competence of the LBD to bind co-activator proteins. We observe the “water trapping” mechanism suggested previously for the atypical inverse agonists and discover a different behavior for the latter when co-activator is present or absent, which might help explain their conflicting data. Additionally, we unveil the same entry/exit path for agonists and inverse agonist into and out of the LBD for RORγ, suggesting it belongs to the type III NHR sub-family.
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11
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Matthews N, Kitao A, Laycock S, Hayward S. Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. J Chem Inf Model 2019; 59:2900-2912. [DOI: 10.1021/acs.jcim.9b00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nick Matthews
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, M6-13, Meguro, Tokyo 152-8550, Japan
| | - Stephen Laycock
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Steven Hayward
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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12
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Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | - Victor Guallar
- Life Science DepartmentBarcelonaSpain
- ICREA, Passeig Lluís Companys 23BarcelonaSpain
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13
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Santiago G, Martínez-Martínez M, Alonso S, Bargiela R, Coscolín C, Golyshin PN, Guallar V, Ferrer M. Rational Engineering of Multiple Active Sites in an Ester Hydrolase. Biochemistry 2018; 57:2245-2255. [DOI: 10.1021/acs.biochem.8b00274] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gerard Santiago
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - Sandra Alonso
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | | | - Víctor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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14
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Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The INMARE Consortium. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. ACS Chem Biol 2018; 13:225-234. [PMID: 29182315 DOI: 10.1021/acschembio.7b00996] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.
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Affiliation(s)
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Gerard Santiago
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Jennifer Chow
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Christoph Gertler
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - José Navarro-Fernández
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Alexander Bollinger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Stephan Thies
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Celia Méndez-García
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | | | | | - Gro E. K. Bjerga
- Uni Research AS, Center for Applied Biotechnology, 5006 Bergen, Norway
| | - Pablo Pérez-García
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Tran Hai
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Mercedes V. Del Pozo
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Runar Stokke
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Ida H. Steen
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Boguslaw P. Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, 60439 Illinois, United States
| | - María Alcaide
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Marco Distaso
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Antonio Fernández-Guerra
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- University of Oxford, Oxford e-Research Centre, Oxford, United Kingdom
| | - Frank O. Glöckner
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Olga V. Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, 98122 Messina, Italy
- Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
- Institute for Bio- and Geosciences IBG-1: Biotechnology, Forschunsgzentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Wolfgang R. Streit
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter N. Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Víctor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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15
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Rogawski R, Sergeyev IV, Zhang Y, Tran TH, Li Y, Tong L, McDermott AE. NMR Signal Quenching from Bound Biradical Affinity Reagents in DNP Samples. J Phys Chem B 2017; 121:10770-10781. [PMID: 29116793 PMCID: PMC5842680 DOI: 10.1021/acs.jpcb.7b08274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We characterize the effect of specifically bound biradicals on the NMR spectra of dihydrofolate reductase from E. coli. Dynamic nuclear polarization methods enhance the signal-to-noise of solid state NMR experiments by transferring polarization from unpaired electrons of biradicals to nuclei. There has been recent interest in colocalizing the paramagnetic polarizing agents with the analyte of interest through covalent or noncovalent specific interactions. This experimental approach broadens the scope of dynamic nuclear polarization methods by offering the possibility of selective signal enhancements and the potential to work in a broad range of environments. Paramagnetic compounds can have other effects on the NMR spectroscopy of nearby nuclei, including broadening of nuclear resonances due to the proximity of the paramagnetic agent. Understanding the distance dependence of these interactions is important for the success of the technique. Here we explore paramagnetic signal quenching due to a bound biradical, specifically a biradical-derivatized trimethoprim ligand of E. coli dihydrofolate reductase. Biradical-derivatized trimethoprim has nanomolar affinity for its target, and affords strong and selective signal enhancements in dynamic nuclear polarization experiments. In this work, we show that, although the trimethoprim fragment is well ordered, the biradical (TOTAPOL) moiety is disordered when bound to the protein. The distance dependence in bleaching of NMR signal intensity allows us to detect numerous NMR signals in the protein. We present the possibility that static disorder and electron spin diffusion play roles in this observation, among other contributions. The fact that the majority of signals are observed strengthens the case for the use of high affinity or covalent radicals in dynamic nuclear polarization solid state NMR enhancement.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yinglu Zhang
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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16
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Kotev M, Manuel-Manresa P, Hernando E, Soto-Cerrato V, Orozco M, Quesada R, Pérez-Tomás R, Guallar V. Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. J Chem Inf Model 2017; 57:2089-2098. [PMID: 28763207 DOI: 10.1021/acs.jcim.7b00178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combining computational modeling, de novo compound synthesis, and in vitro and cellular assays, we have performed an inhibition study against the enhancer of zeste homolog 2 (EZH2) histone-lysine N-methyltransferase. This enzyme is an important catalytic component of the PRC2 complex whose alterations have been associated with different cancers. We introduce here several tambjamine-inspired derivatives with low micromolar in vitro activity that produce a significant decrease in histone 3 trimethylation levels in cancer cells. We demonstrate binding at the methyl transfer active site, showing, in addition, that the EZH2 isolated crystal structure is capable of being used in molecular screening studies. Altogether, this work provides a successful molecular model that will help in the identification of new specific EZH2 inhibitors and identify a novel class of tambjamine-derived EZH2 inhibitors with promising activities for their use in cancer treatment.
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Affiliation(s)
- Martin Kotev
- Joint BSC-CRG-IRB Research Program in Computational Biology. Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain
| | - Pilar Manuel-Manresa
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, University of Barcelona , E-08907 Barcelona, Spain
| | - Elsa Hernando
- Department of Chemistry, Faculty of Science, University of Burgos , 09001 Burgos, Spain
| | - Vanessa Soto-Cerrato
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, University of Barcelona , E-08907 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain
| | - Roberto Quesada
- Department of Chemistry, Faculty of Science, University of Burgos , 09001 Burgos, Spain
| | - Ricardo Pérez-Tomás
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, University of Barcelona , E-08907 Barcelona, Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology. Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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17
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Adaptive simulations, towards interactive protein-ligand modeling. Sci Rep 2017; 7:8466. [PMID: 28814780 PMCID: PMC5559483 DOI: 10.1038/s41598-017-08445-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022] Open
Abstract
Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few years hardware and software advances have significantly revamped the use of molecular simulations, we still lack a fast and accurate ab initio description of the binding mechanism in complex systems, available only for up-to-date techniques and requiring several hours or days of heavy computation. Such delay is one of the main limiting factors for a larger penetration of protein dynamics modeling in the pharmaceutical industry. Here we present a game-changing technology, opening up the way for fast reliable simulations of protein dynamics by combining an adaptive reinforcement learning procedure with Monte Carlo sampling in the frame of modern multi-core computational resources. We show remarkable performance in mapping the protein-ligand energy landscape, being able to reproduce the full binding mechanism in less than half an hour, or the active site induced fit in less than 5 minutes. We exemplify our method by studying diverse complex targets, including nuclear hormone receptors and GPCRs, demonstrating the potential of using the new adaptive technique in screening and lead optimization studies.
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18
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Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. Sci Rep 2017; 7:8223. [PMID: 28811548 PMCID: PMC5557796 DOI: 10.1038/s41598-017-08344-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/10/2017] [Indexed: 11/08/2022] Open
Abstract
Bitter taste is one of the basic taste modalities, warning against consuming potential poisons. Bitter compounds activate members of the bitter taste receptor (Tas2r) subfamily of G protein-coupled receptors (GPCRs). The number of functional Tas2rs is species-dependent. Chickens represent an intriguing minimalistic model, because they detect the bitter taste of structurally different molecules with merely three bitter taste receptor subtypes. We investigated the binding modes of several known agonists of a representative chicken bitter taste receptor, ggTas2r1. Because of low sequence similarity between ggTas2r1 and crystallized GPCRs (~10% identity, ~30% similarity at most), the combination of computational approaches with site-directed mutagenesis was used to characterize the agonist-bound conformation of ggTas2r1 binding site between TMs 3, 5, 6 and 7. We found that the ligand interactions with N93 in TM3 and/or N247 in TM5, combined with hydrophobic contacts, are typically involved in agonist recognition. Next, the ggTas2r1 structural model was successfully used to identify three quinine analogues (epiquinidine, ethylhydrocupreine, quinidine) as new ggTas2r1 agonists. The integrated approach validated here may be applicable to additional cases where the sequence identity of the GPCR of interest and the existing experimental structures is low.
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19
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Sulimov AV, Zheltkov DA, Oferkin IV, Kutov DC, Katkova EV, Tyrtyshnikov EE, Sulimov VB. Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms. Comput Struct Biotechnol J 2017; 15:275-285. [PMID: 28377797 PMCID: PMC5367798 DOI: 10.1016/j.csbj.2017.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/28/2017] [Indexed: 11/28/2022] Open
Abstract
We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.
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Affiliation(s)
- Alexey V Sulimov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Dmitry A Zheltkov
- Faculty of Computational Mathematics and Cybernetics of Lomonosov Moscow State University, Leninskie Gory 1, Bldg. 52, Moscow 119992, Russia
| | - Igor V Oferkin
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia
| | - Danil C Kutov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Ekaterina V Katkova
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
| | - Eugene E Tyrtyshnikov
- Faculty of Computational Mathematics and Cybernetics of Lomonosov Moscow State University, Leninskie Gory 1, Bldg. 52, Moscow 119992, Russia; Institute of Numerical Mathematics of Russian Academy of Sciences, Gubkin Street 8, Moscow, 119333, Russia
| | - Vladimir B Sulimov
- Dimonta, Ltd, Nagornaya Street 15, Bldg. 8, Moscow 117186, Russia; Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg. 4, Moscow 119992, Russia
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20
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Hayes TW, Moal IH. Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method. J Chem Theory Comput 2017; 13:1401-1410. [DOI: 10.1021/acs.jctc.6b01110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas W. Hayes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, United Kingdom
| | - Iain H. Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, United Kingdom
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21
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Cappel D, Hall ML, Lenselink EB, Beuming T, Qi J, Bradner J, Sherman W. Relative Binding Free Energy Calculations Applied to Protein Homology Models. J Chem Inf Model 2016; 56:2388-2400. [PMID: 28024402 PMCID: PMC5777225 DOI: 10.1021/acs.jcim.6b00362] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with full system flexibility and offers promise for the general application of FEP to homology models, although additional validation studies should be performed to further understand the limitations of the method and the scenarios where FEP will work best.
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Affiliation(s)
- Daniel Cappel
- Schrödinger GmbH, Dynamostraße 13, 68165 Mannheim, Germany
| | - Michelle Lynn Hall
- Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Eelke B. Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Thijs Beuming
- Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States
| | - James Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States
| | - Woody Sherman
- Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States
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22
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The unravelling of the complex pattern of tyrosinase inhibition. Sci Rep 2016; 6:34993. [PMID: 27725765 PMCID: PMC5057104 DOI: 10.1038/srep34993] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/22/2016] [Indexed: 12/28/2022] Open
Abstract
Tyrosinases are responsible for melanin formation in all life domains. Tyrosinase inhibitors are used for the prevention of severe skin diseases, in skin-whitening creams and to avoid fruit browning, however continued use of many such inhibitors is considered unsafe. In this study we provide conclusive evidence of the inhibition mechanism of two well studied tyrosinase inhibitors, KA (kojic acid) and HQ (hydroquinone), which are extensively used in hyperpigmentation treatment. KA is reported in the literature with contradicting inhibition mechanisms, while HQ is described as both a tyrosinase inhibitor and a substrate. By visualization of KA and HQ in the active site of TyrBm crystals, together with molecular modeling, binding constant analysis and kinetic experiments, we have elucidated their mechanisms of inhibition, which was ambiguous for both inhibitors. We confirm that while KA acts as a mixed inhibitor, HQ can act both as a TyrBm substrate and as an inhibitor.
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23
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Massink A, Louvel J, Adlere I, van Veen C, Huisman BJH, Dijksteel GS, Guo D, Lenselink EB, Buckley BJ, Matthews H, Ranson M, Kelso M, IJzerman AP. 5′-Substituted Amiloride Derivatives as Allosteric Modulators Binding in the Sodium Ion Pocket of the Adenosine A2A Receptor. J Med Chem 2016; 59:4769-77. [DOI: 10.1021/acs.jmedchem.6b00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Arnault Massink
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | - Julien Louvel
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | - Ilze Adlere
- Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia
| | - Corine van Veen
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | - Berend J. H. Huisman
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | - Gabrielle S. Dijksteel
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | - Dong Guo
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | - Eelke B. Lenselink
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
| | | | | | | | | | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, LACDR, Leiden University, 2300 RA Leiden, The Netherlands
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24
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Hosseini A, Alibés A, Noguera-Julian M, Gil V, Paredes R, Soliva R, Orozco M, Guallar V. Computational Prediction of HIV-1 Resistance to Protease Inhibitors. J Chem Inf Model 2016; 56:915-23. [DOI: 10.1021/acs.jcim.5b00667] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ali Hosseini
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Andreu Alibés
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri i Reixac 8, 08028 Barcelona, Spain
| | - Marc Noguera-Julian
- IrsiCaixa
AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
- Universitat de Vic − Universitat Central de Catalunya, 08500 Vic, Catalonia, Spain
| | - Victor Gil
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Roger Paredes
- IrsiCaixa
AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
- Universitat de Vic − Universitat Central de Catalunya, 08500 Vic, Catalonia, Spain
| | - Robert Soliva
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Modesto Orozco
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri i Reixac 8, 08028 Barcelona, Spain
- Departament
de Bioquímica, Universitat de Barcelona, Avgda Diagona 647, 08029 Barcelona, Spain
| | - Victor Guallar
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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25
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Grebner C, Iegre J, Ulander J, Edman K, Hogner A, Tyrchan C. Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design. J Chem Inf Model 2016; 56:774-87. [DOI: 10.1021/acs.jcim.5b00744] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christoph Grebner
- CVMD Innovative Medicine, ‡RIA Innovative Medicine, and §Discovery Science, AstraZeneca R&D, 43283 Mölndal, Sweden
| | - Jessica Iegre
- CVMD Innovative Medicine, ‡RIA Innovative Medicine, and §Discovery Science, AstraZeneca R&D, 43283 Mölndal, Sweden
| | - Johan Ulander
- CVMD Innovative Medicine, ‡RIA Innovative Medicine, and §Discovery Science, AstraZeneca R&D, 43283 Mölndal, Sweden
| | - Karl Edman
- CVMD Innovative Medicine, ‡RIA Innovative Medicine, and §Discovery Science, AstraZeneca R&D, 43283 Mölndal, Sweden
| | - Anders Hogner
- CVMD Innovative Medicine, ‡RIA Innovative Medicine, and §Discovery Science, AstraZeneca R&D, 43283 Mölndal, Sweden
| | - Christian Tyrchan
- CVMD Innovative Medicine, ‡RIA Innovative Medicine, and §Discovery Science, AstraZeneca R&D, 43283 Mölndal, Sweden
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26
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Kotev M, Lecina D, Tarragó T, Giralt E, Guallar V. Unveiling prolyl oligopeptidase ligand migration by comprehensive computational techniques. Biophys J 2015; 108:116-25. [PMID: 25564858 DOI: 10.1016/j.bpj.2014.11.3453] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 01/03/2023] Open
Abstract
Prolyl oligopeptidase (POP) is a large 80 kDa protease, which cleaves oligopeptides at the C-terminal side of proline residues and constitutes an important pharmaceutical target. Despite the existence of several crystallographic structures, there is an open debate about migration (entrance and exit) pathways for ligands, and their coupling with protein dynamics. Recent studies have shown the capabilities of molecular dynamics and classical force fields in describing spontaneous binding events and nonbiased ligand migration pathways. Due to POP's size and to the buried nature of its active site, an exhaustive sampling by means of conventional long enough molecular dynamics trajectories is still a nearly impossible task. Such a level of sampling, however, is possible with the breakthrough protein energy landscape exploration technique. Here, we present an exhaustive sampling of POP with a known inhibitor, Z-pro-prolinal. In >3000 trajectories Z-pro-prolinal explores all the accessible surface area, showing multiple entrance events into the large internal cavity through the pore in the β-propeller domain. Moreover, we modeled a natural substrate binding and product release by predicting the entrance of an undecapeptide substrate, followed by manual active site cleavage and nonbiased exit of one of the products (a dipeptide). The product exit shows preference from a flexible 18-amino acid residues loop, pointing to an overall mechanism where entrance and exit occur in different sites.
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Affiliation(s)
- Martin Kotev
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Daniel Lecina
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Teresa Tarragó
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Department of Organic Chemistry, University of Barcelona (UB), Barcelona, Spain.
| | - Víctor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Madadkar-Sobhani A, Guallar V. PELE web server: atomistic study of biomolecular systems at your fingertips. Nucleic Acids Res 2013; 41:W322-8. [PMID: 23729469 PMCID: PMC3692087 DOI: 10.1093/nar/gkt454] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein–ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE’s heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.
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Affiliation(s)
- Armin Madadkar-Sobhani
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
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Hosseini A, Espona-Fiedler M, Soto-Cerrato V, Quesada R, Pérez-Tomás R, Guallar V. Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members. PLoS One 2013; 8:e57562. [PMID: 23460874 PMCID: PMC3583838 DOI: 10.1371/journal.pone.0057562] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/26/2013] [Indexed: 12/03/2022] Open
Abstract
Prodigiosin and obatoclax, members of the prodiginines family, are small molecules with anti-cancer properties that are currently under preclinical and clinical trials. The molecular target(s) of these agents, however, is an open question. Combining experimental and computational techniques we find that prodigiosin binds to the BH3 domain in some BCL-2 protein families, which play an important role in the apoptotic programmed cell death. In particular, our results indicate a large affinity of prodigiosin for MCL-1, an anti-apoptotic member of the BCL-2 family. In melanoma cells, we demonstrate that prodigiosin activates the mitochondrial apoptotic pathway by disrupting MCL-1/BAK complexes. Computer simulations with the PELE software allow the description of the induced fit process, obtaining a detailed atomic view of the molecular interactions. These results provide new data to understand the mechanism of action of these molecules, and assist in the development of more specific inhibitors of anti-apoptotic BCL-2 proteins.
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Affiliation(s)
- Ali Hosseini
- Joint BSC-IRB Research Program in Computational Biology, Barcelona, Spain
| | - Margarita Espona-Fiedler
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Vanessa Soto-Cerrato
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Roberto Quesada
- Department of Chemistry, University of Burgos, Burgos, Spain
| | - Ricardo Pérez-Tomás
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail:
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29
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Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine. J Biol Chem 2011; 286:41105-14. [PMID: 21940622 DOI: 10.1074/jbc.m111.282467] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aryl-alcohol oxidase (AAO) is a flavoenzyme responsible for activation of O(2) to H(2)O(2) in fungal degradation of lignin. The AAO crystal structure shows a buried active site connected to the solvent by a hydrophobic funnel-shaped channel, with Phe-501 and two other aromatic residues forming a narrow bottleneck that prevents the direct access of alcohol substrates. However, ligand diffusion simulations show O(2) access to the active site following this channel. Site-directed mutagenesis of Phe-501 yielded a F501A variant with strongly reduced O(2) reactivity. However, a variant with increased reactivity, as shown by kinetic constants and steady-state oxidation degree, was obtained by substitution of Phe-501 with tryptophan. The high oxygen catalytic efficiency of F501W, ∼2-fold that of native AAO and ∼120-fold that of F501A, seems related to a higher O(2) availability because the turnover number was slightly decreased with respect to the native enzyme. Free diffusion simulations of O(2) inside the active-site cavity of AAO (and several in silico Phe-501 variants) yielded >60% O(2) population at 3-4 Å from flavin C4a in F501W compared with 44% in AAO and only 14% in F501A. Paradoxically, the O(2) reactivity of AAO decreased when the access channel was enlarged and increased when it was constricted by introducing a tryptophan residue. This is because the side chain of Phe-501, contiguous to the catalytic histidine (His-502 in AAO), helps to position O(2) at an adequate distance from flavin C4a (and His-502 Nε). Phe-501 substitution with a bulkier tryptophan residue resulted in an increase in the O(2) reactivity of this flavoenzyme.
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Affiliation(s)
- Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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