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Galvani F, Scalvini L, Rivara S, Lodola A, Mor M. Mechanistic Modeling of Monoglyceride Lipase Covalent Modification Elucidates the Role of Leaving Group Expulsion and Discriminates Inhibitors with High and Low Potency. J Chem Inf Model 2022; 62:2771-2787. [PMID: 35580195 PMCID: PMC9198976 DOI: 10.1021/acs.jcim.2c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Inhibition of monoglyceride
lipase (MGL), also known as monoacylglycerol
lipase (MAGL), has emerged as a promising approach for treating neurological
diseases. To gain useful insights in the design of agents with balanced
potency and reactivity, we investigated the mechanism of MGL carbamoylation
by the reference triazole urea SAR629 (IC50 = 0.2 nM) and
two recently described inhibitors featuring a pyrazole (IC50 = 1800 nM) or a 4-cyanopyrazole (IC50 = 8 nM) leaving
group (LG), using a hybrid quantum mechanics/molecular mechanics (QM/MM)
approach. Opposite to what was found for substrate 2-arachidonoyl-sn-glycerol (2-AG), covalent modification of MGL by azole
ureas is controlled by LG expulsion. Simulations indicated that changes
in the electronic structure of the LG greatly affect reaction energetics
with triazole and 4-cyanopyrazole inhibitors following a more accessible
carbamoylation path compared to the unsubstituted pyrazole derivative.
The computational protocol provided reaction barriers able to discriminate
between MGL inhibitors with different potencies. These results highlight
how QM/MM simulations can contribute to elucidating structure–activity
relationships and provide insights for the design of covalent inhibitors.
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Affiliation(s)
- Francesca Galvani
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy.,Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11/A, I-43124 Parma, Italy
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2
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A Review of Recent Developments in Molecular Dynamics Simulations of the Photoelectrochemical Water Splitting Process. Catalysts 2021. [DOI: 10.3390/catal11070807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In this review, we provide a short overview of the Molecular Dynamics (MD) method and how it can be used to model the water splitting process in photoelectrochemical hydrogen production. We cover classical non-reactive and reactive MD techniques as well as multiscale extensions combining classical MD with quantum chemical and continuum methods. Selected examples of MD investigations of various aqueous semiconductor interfaces with a special focus on TiO2 are discussed. Finally, we identify gaps in the current state-of-the-art where further developments will be needed for better utilization of MD techniques in the field of water splitting.
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3
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Synthesis, Molecular Modeling and Biological Evaluation of Metabolically Stable Analogues of the Endogenous Fatty Acid Amide Palmitoylethanolamide. Int J Mol Sci 2020; 21:ijms21239074. [PMID: 33260658 PMCID: PMC7730713 DOI: 10.3390/ijms21239074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022] Open
Abstract
Palmitoylethanolamide (PEA) belongs to the class of N-acylethanolamine and is an endogenous lipid potentially useful in a wide range of therapeutic areas; products containing PEA are licensed for use in humans as a nutraceutical, a food supplement, or food for medical purposes for its analgesic and anti-inflammatory properties demonstrating efficacy and tolerability. However, the exogenously administered PEA is rapidly inactivated; in this process, fatty acid amide hydrolase (FAAH) plays a key role both in hepatic metabolism and in intracellular degradation. So, the aim of the present study was the design and synthesis of PEA analogues that are more resistant to FAAH-mediated hydrolysis. A small library of PEA analogues was designed and tested by molecular docking and density functional theory calculations to find the more stable analogue. The computational investigation identified RePEA as the best candidate in terms of both synthetic accessibility and metabolic stability to FAAH-mediated hydrolysis. The selected compound was synthesized and assayed ex vivo to monitor FAAH-mediated hydrolysis and to confirm its anti-inflammatory properties. 1H-NMR spectroscopy performed on membrane samples containing FAAH in integral membrane protein demonstrated that RePEA is not processed by FAAH, in contrast with PEA. Moreover, RePEA retains PEA’s ability to inhibit LPS-induced cytokine release in both murine N9 microglial cells and human PMA-THP-1 cells.
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4
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Sirirak J, Lawan N, Van der Kamp MW, Harvey JN, Mulholland AJ. Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes. PEERJ PHYSICAL CHEMISTRY 2020. [DOI: 10.7717/peerj-pchem.8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.
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Affiliation(s)
- Jitnapa Sirirak
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
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5
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Lodola A, Callegari D, Scalvini L, Rivara S, Mor M. Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations. Methods Mol Biol 2020; 2114:307-337. [PMID: 32016901 DOI: 10.1007/978-1-0716-0282-9_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a reliable computational method to investigate and characterize chemical reactions occurring in enzymes. From a drug discovery perspective, a thorough understanding of enzyme catalysis appears pivotal to assist the design of inhibitors able to covalently bind one of the residues belonging to the enzyme catalytic machinery. Thanks to the current advances in computer power, and the availability of more efficient algorithms for QM-based simulations, the use of QM/MM methodology is becoming a viable option in the field of covalent inhibitor design. In the present review, we summarized our experience in the field of QM/MM simulations applied to drug design problems which involved the optimization of agents working on two well-known drug targets, namely fatty acid amide hydrolase (FAAH) and epidermal growth factor receptor (EGFR). In this context, QM/MM simulations gave valuable information in terms of geometry (i.e., of transition states and metastable intermediates) and reaction energetics that allowed to correctly predict inhibitor binding orientation and substituent effect on enzyme inhibition. What is more, enzyme reaction modelling with QM/MM provided insights that were translated into the synthesis of new covalent inhibitor featured by a unique combination of intrinsic reactivity, on-target activity, and selectivity.
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Affiliation(s)
- Alessio Lodola
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy.
| | - Donatella Callegari
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Laura Scalvini
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Silvia Rivara
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Marco Mor
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
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6
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Capoferri L, Lodola A, Rivara S, Mor M. Quantum mechanics/molecular mechanics modeling of covalent addition between EGFR-cysteine 797 and N-(4-anilinoquinazolin-6-yl) acrylamide. J Chem Inf Model 2015; 55:589-99. [PMID: 25658136 DOI: 10.1021/ci500720e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer. They covalently bind a noncatalytic cysteine (Cys797) at the surface of EGFR active site by an acrylamide warhead. Herein, we used a hybrid quantum mechanics/molecular mechanics (QM/MM) potential in combination with umbrella sampling in the path-collective variable space to investigate the mechanism of alkylation of Cys797 by the prototypical covalent inhibitor N-(4-anilinoquinazolin-6-yl) acrylamide. Calculations show that Cys797 reacts with the acrylamide group of the inhibitor through a direct addition mechanism, with Asp800 acting as a general base/general acid in distinct steps of the reaction. The obtained reaction free energy is negative (ΔA = -12 kcal/mol) consistent with the spontaneous and irreversible alkylation of Cys797 by N-(4-anilinoquinazolin-6-yl) acrylamide. Our calculations identify desolvation of Cys797 thiolate anion as a key step of the alkylation process, indicating that changes in the intrinsic reactivity of the acrylamide would have only a minor impact on the inhibitor potency.
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Affiliation(s)
- Luigi Capoferri
- Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy
| | - Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy
| | - Silvia Rivara
- Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy
| | - Marco Mor
- Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy
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7
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Palermo G, Campomanes P, Cavalli A, Rothlisberger U, De Vivo M. Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion. J Phys Chem B 2014; 119:789-801. [DOI: 10.1021/jp5052276] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Giulia Palermo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Andrea Cavalli
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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8
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Palermo G, Rothlisberger U, Cavalli A, De Vivo M. Computational insights into function and inhibition of fatty acid amide hydrolase. Eur J Med Chem 2014; 91:15-26. [PMID: 25240419 DOI: 10.1016/j.ejmech.2014.09.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/01/2014] [Accepted: 09/11/2014] [Indexed: 01/11/2023]
Abstract
The Fatty Acid Amide Hydrolase (FAAH) enzyme is a membrane-bound serine hydrolase responsible for the deactivating hydrolysis of a family of naturally occurring fatty acid amides. FAAH is a critical enzyme of the endocannabinoid system, being mainly responsible for regulating the level of its main cannabinoid substrate anandamide. For this reason, pharmacological inhibition of FAAH, which increases the level of endogenous anandamide, is a promising strategy to cure a variety of diseases including pain, inflammation, and cancer. Much structural, mutagenesis, and kinetic data on FAAH has been generated over the last couple of decades. This has prompted several informative computational investigations to elucidate, at the atomic-level, mechanistic details on catalysis and inhibition of this pharmaceutically relevant enzyme. Here, we review how these computational studies - based on classical molecular dynamics, full quantum mechanics, and hybrid QM/MM methods - have clarified the binding and reactivity of some relevant substrates and inhibitors of FAAH. We also discuss the experimental implications of these computational insights, which have provided a thoughtful elucidation of the complex physical and chemical steps of the enzymatic mechanism of FAAH. Finally, we discuss how computations have been helpful for building structure-activity relationships of potent FAAH inhibitors.
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Affiliation(s)
- Giulia Palermo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy; Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy; Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Marco De Vivo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
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9
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Bueren-Calabuig JA, Pierdominici-Sottile G, Roitberg AE. Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study. J Phys Chem B 2014; 118:5807-16. [PMID: 24814976 PMCID: PMC4051249 DOI: 10.1021/jp412294r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 05/08/2014] [Indexed: 12/02/2022]
Abstract
Chagas' disease, also known as American trypanosomiasis, is a lethal, chronic disease that currently affects more than 10 million people in Central and South America. The trans-sialidase from Trypanosoma cruzi (T. cruzi, TcTS) is a crucial enzyme for the survival of this parasite: sialic acids from the host are transferred to the cell surface glycoproteins of the trypanosome, thereby evading the host's immune system. On the other hand, the sialidase of T. rangeli (TrSA), which shares 70% sequence identity with TcTS, is a strict hydrolase and shows no trans-sialidase activity. Therefore, TcTS and TrSA represent an excellent framework to understand how different catalytic activities can be achieved with extremely similar structures. By means of combined quantum mechanics-molecular mechanics (QM/MM, SCC-DFTB/Amberff99SB) calculations and umbrella sampling simulations, we investigated the hydrolysis mechanisms of TcTS and TrSA and computed the free energy profiles of these reactions. The results, together with our previous computational investigations, are able to explain the catalytic mechanism of sialidases and describe how subtle differences in the active site make TrSA a strict hydrolase and TcTS a more efficient trans-sialidase.
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Affiliation(s)
- Juan A. Bueren-Calabuig
- Department
of Chemistry, Quantum Theory Project, University
of Florida, Gainesville, Florida 32611, United
States
| | | | - Adrian E. Roitberg
- Department
of Chemistry, Quantum Theory Project, University
of Florida, Gainesville, Florida 32611, United
States
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10
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Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. J Chem Theory Comput 2014; 10:1608-22. [PMID: 26580373 DOI: 10.1021/ct401015e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the hairpin ribozyme by evaluating potential and free energy surfaces of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38 (A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as a general acid which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Møller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d-PhoT and SCC-DFTBPR methods provided acceptable activation barriers with respect to the SCS-MP2 data but predicted significantly different reaction pathways. DFT functionals (BLYP and MPW1K) yielded the same reaction pathway as the SCS-MP2 method. The activation barriers were slightly underestimated by the GGA BLYP functional, although with accuracy comparable to the semiempirical methods. The SCS-MP2 method and hybrid MPW1K functional gave activation barriers that were closest to those derived from experimentally measured rate constants.
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Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics , Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
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11
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Chudyk EI, Dyguda-Kazimierowicz E, Langner KM, Sokalski WA, Lodola A, Mor M, Sirirak J, Mulholland AJ. Nonempirical Energetic Analysis of Reactivity and Covalent Inhibition of Fatty Acid Amide Hydrolase. J Phys Chem B 2013; 117:6656-66. [DOI: 10.1021/jp401834v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ewa I. Chudyk
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | | | - Karol M. Langner
- Institute of Physical & Theoretical Chemistry, Wrocław University of Technology, 50-370 Wrocław, Poland
- Department of Molecular
Physiology
and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - W. Andrzej Sokalski
- Institute of Physical & Theoretical Chemistry, Wrocław University of Technology, 50-370 Wrocław, Poland
| | - Alessio Lodola
- Dipartimento Farmaceutico, Università degli Studi di Parma, 43100 Parma,
Italy
| | - Marco Mor
- Dipartimento Farmaceutico, Università degli Studi di Parma, 43100 Parma,
Italy
| | - Jitnapa Sirirak
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
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12
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Lodola A, Capoferri L, Rivara S, Tarzia G, Piomelli D, Mulholland A, Mor M. Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors. J Med Chem 2013; 56:2500-12. [PMID: 23425199 DOI: 10.1021/jm301867x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Carbamate and urea derivatives are important classes of fatty acid amide hydrolase (FAAH) inhibitors that carbamoylate the active-site nucleophile Ser241. In the present work, the reactivation mechanism of carbamoylated FAAH is investigated by means of a quantum mechanics/molecular mechanics (QM/MM) approach. The potential energy surfaces for decarbamoylation of FAAH covalent adducts, derived from the O-aryl carbamate URB597 and from the N-piperazinylurea JNJ1661610, were calculated and compared to that for deacylation of FAAH acylated by the substrate oleamide. Calculations show that a carbamic group bound to Ser241 prevents efficient stabilization of transition states of hydrolysis, leading to large increments in the activation barrier. Moreover, the energy barrier for the piperazine carboxylate was significantly lower than that for the cyclohexyl carbamate derived from URB597. This is consistent with experimental data showing slowly reversible FAAH inhibition for the N-piperazinylurea inhibitor and irreversible inhibition for URB597.
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Affiliation(s)
- Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma, I-43124 Parma, Italy
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13
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Palermo G, Campomanes P, Neri M, Piomelli D, Cavalli A, Rothlisberger U, De Vivo M. Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis. J Chem Theory Comput 2013; 9:1202-13. [PMID: 26588763 DOI: 10.1021/ct300611q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine hydrolase, fatty acid amide hydrolase (FAAH), is responsible for the intracellular degradation of anandamide and other bioactive fatty acid ethanolamides involved in the regulation of pain, inflammation, and other pathophysiological processes. The catalytic site of FAAH is composed of multiple cavities with mixed hydrophobic and hydrophilic properties, the role of which remains incompletely understood. Anandamide is thought to enter the active site through a "membrane-access" (MA) channel and position its flexible fatty acyl chain in a highly hydrophobic "acyl chain-binding" (AB) cavity to allow for hydrolysis to occur. Using microsecond molecular dynamics (MD) simulations of FAAH embedded in a realistic membrane/water environment, we show now that anandamide may not lock itself into the AB cavity but may rather assume catalytically significant conformations required for hydrolysis by moving its flexible arachidonoyl tail between the MA and AB cavities. This process is regulated by a phenylalanine residue (Phe432) located at the boundary between the two cavities, which may act as a "dynamic paddle." The results identify structural flexibility as a key determinant by which FAAH recognizes its primary lipid substrate.
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Affiliation(s)
- Giulia Palermo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.,Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marilisa Neri
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Daniele Piomelli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.,Department of Anatomy and Neurobiology, University of California, Irvine, California 92697, United States
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.,Department of Pharmaceutical Sciences, University of Bologna, via Belmeloro 6, I-40126 Bologna, Italy
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
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14
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Lodola A, Branduardi D, De Vivo M, Capoferri L, Mor M, Piomelli D, Cavalli A. A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations. PLoS One 2012; 7:e32397. [PMID: 22389698 PMCID: PMC3289653 DOI: 10.1371/journal.pone.0032397] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 01/29/2012] [Indexed: 12/22/2022] Open
Abstract
The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors.
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Affiliation(s)
- Alessio Lodola
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Davide Branduardi
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
| | - Marco De Vivo
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
| | - Luigi Capoferri
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Marco Mor
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Daniele Piomelli
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
- Department of Pharmacology, University of California Irvine, Irvine, California, United States of America
| | - Andrea Cavalli
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
- Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy
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The increasing role of QM/MM in drug discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 87:337-62. [PMID: 22607760 DOI: 10.1016/b978-0-12-398312-1.00011-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Since its first appearance in 1976, the quantum mechanics/molecular mechanics (QM/MM) approach has mostly been used to study the chemical reactions of enzymes, which are frequently the target of drug discovery programs. In principle, a detailed understanding of the enzymatic mechanism should help researchers to design a potent enzyme inhibitor or new drug. However, QM/MM has not yet had a widespread impact on structure-based drug design. This is mostly due to its high computational cost. We expect this to change with the recent and extraordinary increases in computational power, and with the availability of more efficient algorithms for QM/MM calculations. Here, we report on some representative examples of QM/MM studies, including our own research, of pharmaceutically relevant enzymes, such as ribonuclease H and fatty acid amide hydrolase (FAAH). We aim to show how QM/MM has traditionally been used to study enzymatic catalysis. In this regard, we discuss its potential to become a routinely used drug design tool. To support this, we also discuss selected computational studies where QM/MM insights have been helpful in improving the potency of covalent inhibitors of FAAH.
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16
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Mujika JI, Lopez X, Mulholland AJ. Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations. Org Biomol Chem 2011; 10:1207-18. [PMID: 22179261 DOI: 10.1039/c1ob06444d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein splicing is a post-translational process in which a biologically inactive protein is activated by the release of a segment denoted as an intein. The process involves four steps. In the third, the scission of the intein takes place after the cyclization of the last amino acid of the segment, an asparagine. Little is known about the chemical reaction necessary for this cyclization. Experiments demonstrate that two histidines (the penultimate amino acid of the intein, and a histidine located 10 amino acids upstream) are relevant in the cyclization of the asparagine. We have investigated the mechanism and determinants of reaction in the GyrA intein focusing on the requirements for asparagine activation for its cyclization. First, the influence that the protonation states of these two histidines have on the orientation of the asparagine side chain is investigated by means of molecular dynamics simulation. Molecular dynamics simulations using the CHARMM27 force field were carried out on the three possible protonation states for each of these two histidines. The results indicate that the only protonation state in which the conformation of the system is suitable for cyclization is when the penultimate histidine is fully protonated (positively charged), and the upstream histidine is in the His(ε) neutral tautomeric form. The free energy profile for the reaction in which the asparagine is activated by a proton transfer to the upstream histidine is presented, computed by hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics at the SCCDFTB/CHARMM27 level of theory. The calculated free energy barrier for the reaction is 19.0 kcal mol(-1). B3LYP/6-31+G(d) QM/MM single-point calculations give a qualitatively a similar energy profile, although with somewhat higher energy barriers, in good agreement with the value derived from experiment of 25 kcal mol(-1) at 60 °C. QM/MM molecular dynamics simulations of the reactant, activated reactant and intermediate states highlight the importance of the Arg181-Val182-Asp183 segment in catalysing the reaction. Overall, the results indicate that nucleophilic activation of the asparagine for its cyclization by the upstream histidine acting as the base is a plausible mechanism for the C-terminal cleavage in protein splicing.
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Affiliation(s)
- Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC, P. K. 1072, 20080, Donostia, Euskadi, Spain.
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