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Sgrignani J, Cavalli A. Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2. Front Mol Biosci 2021; 8:666626. [PMID: 33996911 PMCID: PMC8119889 DOI: 10.3389/fmolb.2021.666626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 12/23/2022] Open
Abstract
Camostat, nafamostat, and bromhexine are inhibitors of the transmembrane serine protease TMPRSS2. The inhibition of TMPRSS2 has been shown to prevent the viral infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses. However, while camostat and nafamostat inhibit TMPRSS2 by forming a covalent adduct, the mode of action of bromhexine remains unclear. TMPRSS2 is autocatalytically activated from its inactive form, zymogen, through a proteolytic cleavage that promotes the binding of Ile256 to a putative allosteric pocket (A-pocket). Computer simulations, reported here, indicate that Ile256 binding induces a conformational change in the catalytic site, thus providing the atomistic rationale to the activation process of the enzyme. Furthermore, computational docking and molecular dynamics simulations indicate that bromhexine competes with the N-terminal Ile256 for the same binding site, making it a potential allosteric inhibitor. Taken together, these findings provide the atomistic basis for the development of more selective and potent TMPRSS2 inhibitors.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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2
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Garofalo M, Grazioso G, Cavalli A, Sgrignani J. How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs. Molecules 2020; 25:E1756. [PMID: 32290224 PMCID: PMC7180704 DOI: 10.3390/molecules25071756] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023] Open
Abstract
The early and late development of new anticancer drugs, small molecules or peptides can be slowed down by some issues such as poor selectivity for the target or poor ADME properties. Computer-aided drug design (CADD) and target drug delivery (TDD) techniques, although apparently far from each other, are two research fields that can give a significant contribution to overcome these problems. Their combination may provide mechanistic understanding resulting in a synergy that makes possible the rational design of novel anticancer based therapies. Herein, we aim to discuss selected applications, some also from our research experience, in the fields of anticancer small organic drugs and peptides.
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Affiliation(s)
- Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milano, 20133 Milan, Italy
| | - Andrea Cavalli
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
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3
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Oliveira ASF, Shoemark DK, Campello HR, Wonnacott S, Gallagher T, Sessions RB, Mulholland AJ. Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations. Structure 2019; 27:1171-1183.e3. [PMID: 31130483 DOI: 10.1016/j.str.2019.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/28/2019] [Accepted: 04/10/2019] [Indexed: 02/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous system. These receptors have emerged as therapeutic targets in drug discovery for treating several conditions, including Alzheimer's disease, pain, and nicotine addiction. In this in silico study, we use a combination of equilibrium and nonequilibrium molecular dynamics simulations to map dynamic and structural changes induced by nicotine in the human α4β2 nAChR. They reveal a striking pattern of communication between the extracellular binding pockets and the transmembrane domains (TMDs) and show the sequence of conformational changes associated with the initial steps in this process. We propose a general mechanism for signal transduction for Cys-loop receptors: the mechanistic steps for communication proceed firstly through loop C in the principal subunit, and are subsequently transmitted, gradually and cumulatively, to loop F of the complementary subunit, and then to the TMDs through the M2-M3 linker.
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Affiliation(s)
- A Sofia F Oliveira
- School of Biochemistry, University of Bristol, Bristol BS8 1DT, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Hugo Rego Campello
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Susan Wonnacott
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery? Future Med Chem 2019; 11:771-791. [DOI: 10.4155/fmc-2018-0495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Metallo-enzymes are a large class of biomolecules promoting specialized chemical reactions. Quantum-classical quantum mechanics/molecular mechanics molecular dynamics, describing the metal site at quantum mechanics level, while accounting for the rest of system at molecular mechanics level, has an accessible time-scale limited by its computational cost. Hence, it must be integrated with classical molecular dynamics and enhanced sampling simulations to disentangle the functions of metallo-enzymes. In this review, we provide an overview of these computational methods and their capabilities. In particular, we will focus on some systems such as CYP19A1 a Fe-dependent enzyme involved in estrogen biosynthesis, and on Mg2+-dependent DNA/RNA processing enzymes/ribozymes and the spliceosome, a protein-directed ribozyme. This information may guide the discovery of drug-like molecules and genetic manipulation tools.
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Manetti D, Garifulina A, Bartolucci G, Bazzicalupi C, Bellucci C, Chiaramonte N, Dei S, Di Cesare Mannelli L, Ghelardini C, Gratteri P, Spirova E, Shelukhina I, Teodori E, Varani K, Tsetlin V, Romanelli MN. New Rigid Nicotine Analogues, Carrying a Norbornane Moiety, Are Potent Agonists of α7 and α3* Nicotinic Receptors. J Med Chem 2019; 62:1887-1901. [PMID: 30681854 DOI: 10.1021/acs.jmedchem.8b01372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A three-dimensional database search has been applied to design a series of endo- and exo-3-(pyridin-3-yl)bicyclo[2.2.1]heptan-2-amines as nicotinic receptor ligands. The synthesized compounds were tested in radioligand binding assay on rat cortex against [3H]-cytisine and [3H]-methyllycaconitine to measure their affinity for α4β2* and α7* nicotinic receptors. The new derivatives showed some preference for the α4β2* over the α7* subtype, with their affinity being dependent on the endo/exo isomerism and on the methylation degree of the basic nitrogen. The endo primary amines displayed the lowest Ki values on both receptor subtypes. Selected compounds (1a, 2a, 3a, and 6a) were tested on heterologously expressed α4β2, α7, and α3β2 receptors and on SHSY-5Y cells. Compounds 1a and 2a showed α4β2 antagonistic properties while behaved as full agonists on recombinant α7 and on SHSY5Y cells. On the α3β2 subtype, only the chloro derivative 2a showed full agonist activity and submicromolar potency (EC50 = 0.43 μM). The primary amines described here represent new chemotypes for the α7 and α3* receptor subtypes.
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Affiliation(s)
- Dina Manetti
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Alexandra Garifulina
- Department of Molecular Basis of Neurosignaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya Street 16/10 , 117997 Moscow , Russia
| | - Gianluca Bartolucci
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Carla Bazzicalupi
- Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Cristina Bellucci
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Niccolò Chiaramonte
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Silvia Dei
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Lorenzo Di Cesare Mannelli
- Department of NEUROFARBA, Section of Pharmacology and Toxicology , University of Florence , Viale G Pieraccini 6 , 50139 Firenze , Italy
| | - Carla Ghelardini
- Department of NEUROFARBA, Section of Pharmacology and Toxicology , University of Florence , Viale G Pieraccini 6 , 50139 Firenze , Italy
| | - Paola Gratteri
- Department of NEUROFARBA, Laboratory of Molecular Modeling Cheminformatics & QSAR , University of Firenze , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Ekaterina Spirova
- Department of Molecular Basis of Neurosignaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya Street 16/10 , 117997 Moscow , Russia
| | - Irina Shelukhina
- Department of Molecular Basis of Neurosignaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya Street 16/10 , 117997 Moscow , Russia
| | - Elisabetta Teodori
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
| | - Katia Varani
- Institute of Pharmacology , University of Ferrara , Via Fossato di Mortara 17-19 , 44100 Ferrara , Italy
| | - Victor Tsetlin
- Department of Molecular Basis of Neurosignaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya Street 16/10 , 117997 Moscow , Russia
| | - Maria Novella Romanelli
- Department of Neuroscience, Psychology, Drug Research and Child's Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Via Ugo Schiff 6 , 50019 Sesto Fiorentino , Italy
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Abstract
Today, the development of new drugs is a challenging task of science. Researchers already applied molecular docking in the drug design field to simulate ligand- receptor interactions. Docking is a term used for computational schemes that attempt to find the “best” matching between two molecules in a complex formed from constituent molecules. It has a wide range of uses and applications in drug discovery. However, some defects still exist; the accuracy and speed of docking calculation is a challenge to explore and these methods can be enhanced as a solution to docking problem. The molecular docking problem can be defined as follows: Given the atomic coordinates of two molecules, predict their “correct” bound association. The chapter discusses common challenges critical aspects of docking method such as ligand- and receptor- conformation, flexibility and cavity detection, etc. It emphasis to the challenges and inadequacies with the theories behind as well as the examples.
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Ghasemi JB, Abdolmaleki A, Shiri F. Molecular Docking Challenges and Limitations. ADVANCES IN MEDICAL TECHNOLOGIES AND CLINICAL PRACTICE 2016. [DOI: 10.4018/978-1-5225-0362-0.ch003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Today, the development of new drugs is a challenging task of science. Researchers already applied molecular docking in the drug design field to simulate ligand- receptor interactions. Docking is a term used for computational schemes that attempt to find the “best” matching between two molecules in a complex formed from constituent molecules. It has a wide range of uses and applications in drug discovery. However, some defects still exist; the accuracy and speed of docking calculation is a challenge to explore and these methods can be enhanced as a solution to docking problem. The molecular docking problem can be defined as follows: Given the atomic coordinates of two molecules, predict their “correct” bound association. The chapter discusses common challenges critical aspects of docking method such as ligand- and receptor- conformation, flexibility and cavity detection, etc. It emphasis to the challenges and inadequacies with the theories behind as well as the examples.
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Sgrignani J, Olsson S, Ekonomiuk D, Genini D, Krause R, Catapano CV, Cavalli A. Molecular Determinants for Unphosphorylated STAT3 Dimerization Determined by Integrative Modeling. Biochemistry 2015; 54:5489-501. [DOI: 10.1021/bi501529x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jacopo Sgrignani
- Institute of Research in Biomedicine (IRB) and Universitá della Svizzera italiana (USI), Via Vincenzo
Vela 6, CH-6500 Bellinzona, Switzerland
| | - Simon Olsson
- Institute of Research in Biomedicine (IRB) and Universitá della Svizzera italiana (USI), Via Vincenzo
Vela 6, CH-6500 Bellinzona, Switzerland
- Laboratorium
für Physikalische Chemie, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Dariusz Ekonomiuk
- Institute of Research in Biomedicine (IRB) and Universitá della Svizzera italiana (USI), Via Vincenzo
Vela 6, CH-6500 Bellinzona, Switzerland
| | - Davide Genini
- IOR Institute of Oncology Research, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Rolf Krause
- Institute
of Computational Science, Faculty of Informatics, Universitá della Svizzera Italiana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Carlo V. Catapano
- IOR Institute of Oncology Research, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute of Research in Biomedicine (IRB) and Universitá della Svizzera italiana (USI), Via Vincenzo
Vela 6, CH-6500 Bellinzona, Switzerland
- Department
of Chemistry, University of Cambridge, Lansfield Road, Cambridge CB2 1EW, U.K
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9
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Sgrignani J, Novati B, Colombo G, Grazioso G. Covalent docking of selected boron-based serine beta-lactamase inhibitors. J Comput Aided Mol Des 2015; 29:441-50. [DOI: 10.1007/s10822-015-9834-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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10
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Sgrignani J, Bon M, Colombo G, Magistrato A. Computational approaches elucidate the allosteric mechanism of human aromatase inhibition: a novel possible route to Small-molecule regulation of CYP450s activities? J Chem Inf Model 2014; 54:2856-68. [PMID: 25178092 DOI: 10.1021/ci500425y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human aromatase (HA) is a P450 cytochrome (CYP) with an essential role in estrogen biosynthesis. Since more than 70% of breast cancers are positive for estrogenic receptor (ER), the reduction of estrogen physiological concentrations through HA inhibition is one of most important therapeutic strategies against this cancer type. Recently, experimental evidence showed that selected taxmoxifen metabolites, which are typically used as estrogen receptor modulators (SERMs), inhibit HA through an allosteric mechanism. In this work, we present a computational protocol to (i) characterize the structural framework and (ii) define the atomistic details of the determinants for the noncompetitive inhibition mechanism. Our calculations identify two putative binding sites able to efficiently bind all tamoxifen metabolites. Analysis of long-scale molecular dynamics simulations reveal that endoxifen, the most effective noncompetitive inhibitor, induces significant enzyme rigidity by binding in one of the possible peripheral sites. The consequence of this binding event is the suppression of one of the functional enzymatic collective motions associated with breathing of the substrate access channel. Moreover, an internal dynamics-based alignment of HA with six other human cytochromes shows that this collective motion is common to other members of the CYP450 protein family. On this basis, our findings may thus be of help for the development of new (pan)inhibitors for the therapeutic treatment of cancer, targeting and modulating the activity of HA and of estrogen receptor, and may also stimulate the development of new drug design strategies for chemoprevention and chemoprotection via allosteric inhibition of CYP450 proteins.
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Affiliation(s)
- Jacopo Sgrignani
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Milano, Italy
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QM-polarized ligand docking accurately predicts the trend in binding affinity of a series of arylmethylene quinuclidine-like derivatives at the α4β2 and α3β4 nicotinic acetylcholine receptors (nAChRs). Bioorg Med Chem Lett 2013; 23:4842-7. [DOI: 10.1016/j.bmcl.2013.06.094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/20/2013] [Accepted: 06/27/2013] [Indexed: 11/20/2022]
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12
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Yang X, Xie H, Chen J, Li X. Anionic Phenolic Compounds Bind Stronger with Transthyretin than Their Neutral Forms: Nonnegligible Mechanisms in Virtual Screening of Endocrine Disrupting Chemicals. Chem Res Toxicol 2013; 26:1340-7. [DOI: 10.1021/tx4001557] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xianhai Yang
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hongbin Xie
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xuehua Li
- Key Laboratory
of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
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Mechanism of falcipain-2 inhibition by α,β-unsaturated benzo[1,4]diazepin-2-one methyl ester. J Comput Aided Mol Des 2012; 26:1035-43. [PMID: 22965332 PMCID: PMC7088093 DOI: 10.1007/s10822-012-9596-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/27/2012] [Indexed: 01/11/2023]
Abstract
Falcipain-2 (FP-2) is a papain-family cysteine protease of Plasmodium falciparum whose primary function is to degrade the host red cell hemoglobin, within the food vacuole, in order to provide free amino acids for parasite protein synthesis. Additionally it promotes host cell rupture by cleaving the skeletal proteins of the erythrocyte membrane. Therefore, the inhibition of FP-2 represents a promising target in the search of novel anti-malarial drugs. A potent FP-2 inhibitor, characterized by the presence in its structure of the 1,4-benzodiazepine scaffold and an α,β-unsaturated methyl ester moiety capable to react with the Cys42 thiol group located in the active site of FP-2, has been recently reported in literature. In order to study in depth the inhibition mechanism triggered by this interesting compound, we carried out, through ONIOM hybrid calculations, a computational investigation of the processes occurring when the inhibitor targets the enzyme and eventually leads to an irreversible covalent Michael adduct. Each step of the reaction mechanism has been accurately characterized and a detailed description of each possible intermediate and transition state along the pathway has been reported.
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Sgrignani J, Magistrato A. Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study. J Chem Inf Model 2012; 52:1595-606. [DOI: 10.1021/ci300151h] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-Democritos National Simulation Center c/o International Studies for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste
(TS), Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o International Studies for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste
(TS), Italy
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15
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Antony J, Grimme S. Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory. J Comput Chem 2012; 33:1730-9. [PMID: 22570225 DOI: 10.1002/jcc.23004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 01/31/2023]
Abstract
Dispersion corrected density functional theory (DFT-D3) is used for fully ab initio protein-ligand (PL) interaction energy calculation via molecular fractionation with conjugated caps (MFCC) and applied to PL complexes from the PDB comprising 3680, 1798, and 1060 atoms. Molecular fragments with n amino acids instead of one in the original MFCC approach are considered, thereby allowing for estimating the three-body and higher many-body terms. n > 1 is recommended both in terms of accuracy and efficiency of MFCC. For neutral protein side-chains, the computed PL interaction energy is visibly independent of the fragment length n. The MFCC fractionation error is determined by comparison to a full-system calculation for the 1060 atoms containing PL complex. For charged amino acid side-chains, the variation of the MFCC result with n is increased. For these systems, using a continuum solvation model with a dielectricity constant typical for protein environments (ϵ = 4) reduces both the variation with n and improves the stability of the DFT calculations considerably. The PL interaction energies for two typical complexes obtained ab initio for the first time are found to be rather large (-30 and -54 kcal/mol).
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Affiliation(s)
- Jens Antony
- Universität Münster, Organisch-Chemisches Institut, Germany
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16
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Dallanoce C, Magrone P, Matera C, Frigerio F, Grazioso G, De Amici M, Fucile S, Piccari V, Frydenvang K, Pucci L, Gotti C, Clementi F, De Micheli C. Design, synthesis, and pharmacological characterization of novel spirocyclic quinuclidinyl-Δ2-isoxazoline derivatives as potent and selective agonists of α7 nicotinic acetylcholine receptors. ChemMedChem 2011; 6:889-903. [PMID: 21365765 DOI: 10.1002/cmdc.201000514] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/13/2011] [Indexed: 11/08/2022]
Abstract
A set of racemic spirocyclic quinuclidinyl-Δ(2)-isoxazoline derivatives was synthesized using a 1,3-dipolar cycloaddition-based approach. Target compounds were assayed for binding affinity toward rat neuronal homomeric (α7) and heteromeric (α4β2) nicotinic acetylcholine receptors. Δ(2) -Isoxazolines 3 a (3-Br), 6 a (3-OMe), 5 a (3-Ph), 8 a (3-OnPr), and 4 a (3-Me) were the ligands with the highest affinity for the α7 subtype (K(i) values equal to 13.5, 14.2, 25.0, 71.6, and 96.2 nM, respectively), and showed excellent α7 versus α4β2 subtype selectivity. These compounds, tested in electrophysiological experiments against human α7 and α4β2 receptors stably expressed in cell lines, behaved as partial α7 agonists with varying levels of potency. The two enantiomers of (±)-3-methoxy-1-oxa-2,7-diaza-7,10-ethanospiro[4.5]dec-2-ene sesquifumarate 6 a were prepared using (+)-dibenzoyl-L- or (-)-dibenzoyl-D-tartaric acid as resolving agents. Enantiomer (R)-(-)-6 a was found to be the eutomer, with K(i) values of 4.6 and 48.7 nM against rat and human α7 receptors, respectively.
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Affiliation(s)
- Clelia Dallanoce
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Università degli Studi di Milano, Milan, Italy
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17
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Wallrapp FH, Guallar V. Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.27] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Sander T, Bruun AT, Balle T. Docking to flexible nicotinic acetylcholine receptors: A validation study using the acetylcholine binding protein. J Mol Graph Model 2010; 29:415-24. [DOI: 10.1016/j.jmgm.2010.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/28/2010] [Accepted: 08/17/2010] [Indexed: 10/19/2022]
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19
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Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010; 24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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