1
|
Mihalovits LM, Kollár L, Bajusz D, Knez D, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones. Chemphyschem 2024; 25:e202300596. [PMID: 37888491 DOI: 10.1002/cphc.202300596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
Heterocyclic thiones have recently been identified as reversible covalent warheads, consistent with their mild electrophilic nature. Little is known so far about their mechanism of action in labelling nucleophilic sidechains, especially cysteines. The vast number of tractable cysteines promotes a wide range of target proteins to examine; however, our focus was put on functional cysteines. We chose the main protease of SARS-CoV-2 harboring Cys145 at the active site that is a structurally characterized and clinically validated target of covalent inhibitors. We screened an in-house, cysteine-targeting covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole, benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were selected for further investigations with the objective of exploring the mechanism of inhibition of the thiones and using the thoroughly characterized Michael acceptors for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism of covalent cysteine labelling by thione derivatives, which was supported by QM and free energy calculations and by a wide range of experimental results. Our study shows that the molecular recognition step plays a crucial role in the overall binding of both sets of molecules.
Collapse
Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Levente Kollár
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Damijan Knez
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Krištof Bozovičar
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tímea Imre
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Stanislav Gobec
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
| |
Collapse
|
2
|
Cerqueira NMFSA, Neves M, Rocha J, Soares-da Silva P, Palma PN. Inactivation Mechanism of the Fatty Acid Amide Hydrolase Inhibitor BIA 10-2474. Chembiochem 2022; 23:e202200166. [PMID: 35843872 DOI: 10.1002/cbic.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/11/2022] [Indexed: 11/07/2022]
Abstract
BIA 10-2474 is a time-dependent inhibitor of fatty acid amide hydrolase(FAAH) that was under clinical development for the treatment of neurological conditions when the program was terminated after one subject died and four were hospitalized with neurological symptoms during a first-in-human clinical study. The present manuscript describes the mechanism of FAAH inhibition by BIA 10-2474 as a target-specific covalent inhibition, supported by quantum mechanics and molecular modelling studies. The inhibitor incorporates a weakly reactive electrophile which, upon specific binding to the enzyme's active site, is positioned to react readily with the catalytic residues. The reactivity is enhanced on-site by the increased molarity at the reaction site and by specific inductive interactions with FAAH. In the second stage, the inhibitor reacts with the enzyme's catalytic nucleophile to form a covalent enzyme-inhibitor adduct. The hydrolysis of this adduct is shown to be unlikely under physiological conditions, therefore leading to irreversible inactivation of FAAH. The results also reveal the important role played by FAAH Thr236 in the reaction with BIA 10-2474, which is specific to FAAH and is not present in other serine hydrolases.
Collapse
Affiliation(s)
- Nuno M F S A Cerqueira
- Department of Research & Development BIAL, Portela & Cª. S.A., S. Mamede do Coronado, Portugal
| | - Marco Neves
- Department of Research & Development BIAL, Portela & Cª. S.A., S. Mamede do Coronado, Portugal
| | - Juliana Rocha
- BioSIM, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Patrício Soares-da Silva
- Department of Research & Development BIAL, Portela & Cª. S.A., S. Mamede do Coronado, Portugal
- Department of Biomedicine, Unit of Pharmacology & Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal
- MedInUP - Center for Drug Discovery and Innovative Medicines, University of Porto, Porto, Portugal
| | - P Nuno Palma
- Department of Research & Development BIAL, Portela & Cª. S.A., S. Mamede do Coronado, Portugal
| |
Collapse
|
3
|
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
![]()
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.
Collapse
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
| |
Collapse
|
4
|
Ramos-Guzmán CA, Velázquez-Libera JL, Ruiz-Pernía JJ, Tuñón I. Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition. J Chem Theory Comput 2022; 18:4005-4013. [PMID: 35549334 PMCID: PMC9115880 DOI: 10.1021/acs.jctc.2c00294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Cysteine proteases are an important target for the development of inhibitors that could
be used as drugs to regulate the activity of these kinds of enzymes involved in many
diseases, including COVID-19. For this reason, it is important to have methodological
tools that allow a detailed study of their activity and inhibition, combining
computational efficiency and accuracy. We here explore the performance of different
quantum mechanics/molecular mechanics methods to explore the inhibition reaction
mechanism of the SARS-CoV-2 3CL protease with a hydroxymethyl ketone derivative. We
selected two density functional theory (DFT) functionals (B3LYP and M06-2X), two
semiempirical Hamiltonians (AM1d and PM6), and two tight-binding DFT methods (DFTB3 and
GFN2-xTB) to explore the free energy landscape associated with this reaction. We show
that it is possible to obtain an accurate description combining molecular dynamics
simulations performed using tight-binding DFT methods and single-point energy
corrections at a higher QM description. The use of a computational strategy that
provides reliable results at a reasonable computational cost could assist the in silico
screening of possible candidates during the design of new drugs directed against
cysteine proteases.
Collapse
Affiliation(s)
- Carlos A Ramos-Guzmán
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| | - José Luis Velázquez-Libera
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain.,Departamento de Bioinformática, Facultad de Ingeniería, Centro de Bioinformática, Simulación y Modelado (CBSM), Universidad de Talca, Talca 3460000, Chile
| | - J Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| |
Collapse
|
5
|
Akher FB, Farrokhzadeh A, Ravenscroft N, Kuttel MM. Deciphering the Mechanism of Binding Selectivity of Chlorofluoroacetamide-Based Covalent Inhibitors toward L858R/T790M Resistance Mutation. J Chem Inf Model 2022; 62:997-1013. [PMID: 35119858 DOI: 10.1021/acs.jcim.1c01399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalent modification of the oncogenic mutant epidermal growth factor receptor (EGFR) by small molecules is an efficient strategy for achieving an enhanced and sustained pharmacological effect in the treatment of non-small-cell lung cancer. NSP-037 (18), an irreversible inhibitor of the L858R/T790M double-mutant EGFR (EGFRDM) using α-chlorofluoroacetamide (CFA) as a novel warhead, has seven times the inhibition selectivity for EGFRDM over the wild type (EGFRWT), as compared to clinically approved osimertinib (7). Here, we employ multiple computational approaches to elucidate the mechanism underlining this improved selectivity, as well as the effect of CFA on the selectivity enhancement of inhibitor 18 over 7. We find that EGFRDM undergoes significantly larger conformational changes than EGFRWT upon binding to 18. The conformational stability of the diamine side chain and the CFA motif of 18 in the orthosteric site of EGFRDM is identified as key for the disparate binding mechanism and inhibitory prowess of 18 with respect to EGFRWT and EGFRDM and 18's higher selectivity than 7. The binding free energy of the 18-bound complexes is -6.38 kcal/mol greater than that of the 7-bound complexes, explaining the difference in selectivity of these inhibitors. Further, free energy decomposition analysis indicates that the electrostatic contribution of key residues plays an important role in the 18-bound complexes. QM/MM calculations show that the most favored mechanism for the Cys797 alkylation reaction is the direct displacement mechanism through a CFA-based inhibitor, producing a reaction with the lowest energy barrier and most stable product.
Collapse
Affiliation(s)
- Farideh Badichi Akher
- Department of Computer Science, University of Cape Town, Cape Town 7700, South Africa.,Department of Chemistry, University of Cape Town, Cape Town 7700, South Africa.,Department of Biochemistry & Molecular Biology, University of Dalhousie, Halifax, NS B3H 4R2, Canada
| | | | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Cape Town 7700, South Africa
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Cape Town 7700, South Africa
| |
Collapse
|
6
|
Kulkarni PU, Shah H, Vyas VK. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery. Mini Rev Med Chem 2021; 22:1096-1107. [PMID: 34620049 DOI: 10.2174/1389557521666211007115250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022]
Abstract
Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.
Collapse
Affiliation(s)
- Prajakta U Kulkarni
- School of Pharmacy, ITM (SLS) Baroda University, Vadodara 391510, Gujarat. India
| | - Harshil Shah
- Department of Pharmaceutical Chemistry, Sardar Patel College of Pharmacy, Bakrol, Anand 388315, Gujarat. India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat. India
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Bononi G, Poli G, Rizzolio F, Tuccinardi T, Macchia M, Minutolo F, Granchi C. An updated patent review of monoacylglycerol lipase (MAGL) inhibitors (2018-present). Expert Opin Ther Pat 2020; 31:153-168. [PMID: 33085920 DOI: 10.1080/13543776.2021.1841166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Monoacylglycerol lipase (MAGL) belongs to the endocannabinoid system and is responsible for the inactivation of endocannabinoid 2-arachidonoylglycerol. Importantly, it was found that MAGL degradation of lipids in cancer cells enhances the availability of free fatty acids for new cellular membrane formation and pro-oncogenic lipid modulators. The multifaceted role of MAGL has greatly stimulated the search for MAGL inhibitors, which could be effective to treat diseases, such as inflammation, neurodegeneration and cancer. AREAS COVERED This review covers patents published since 2018 up to now, concerning new MAGL inhibitors and their potential therapeutic applications. EXPERT OPINION In the years 2018-2020, several well-known chemical scaffolds of MAGL inhibitors have been further optimized and developed and some new chemical classes have also been identified as MAGL inhibitors. Moreover, an increasing number of scientific publications covering MAGL inhibitors is focused on MAGL-specific positron emission tomography (PET) ligands. The numerous efforts of pharmaceutical companies and academic research groups finalized to find new potent MAGL inhibitors confirm that this research area is rapidly growing. Nevertheless, most of the patented compounds still belong to the large group of irreversible MAGL inhibitors, highlighting that the development of reversible MAGL inhibitors is still an unmet pharmaceutical need.
Collapse
Affiliation(s)
- Giulia Bononi
- Department of Pharmacy, University of Pisa , Pisa, Italy
| | - Giulio Poli
- Department of Pharmacy, University of Pisa , Pisa, Italy
| | - Flavio Rizzolio
- Pathology Unit, Centro Di Riferimento Oncologico Di Aviano (CRO) IRCCS , Aviano, Italy.,Department of Molecular Science and Nanosystems, Ca' Foscari University , Venezia, Italy
| | | | - Marco Macchia
- Department of Pharmacy, University of Pisa , Pisa, Italy
| | | | | |
Collapse
|
9
|
Scalvini L, Ghidini A, Lodola A, Callegari D, Rivara S, Piomelli D, Mor M. N-Acylethanolamine Acid Amidase (NAAA): Mechanism of Palmitoylethanolamide Hydrolysis Revealed by Mechanistic Simulations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02903] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- 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
| | - Andrea Ghidini
- 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
| | - Donatella Callegari
- 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
| | - Daniele Piomelli
- Department of Anatomy and Neurobiology, University of California, Irvine, California 92697-4625, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-4625, United States
- Department of Biological Chemistry and Molecular Biology, University of California, Irvine, California 92697-4625, United States
| | - 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
| |
Collapse
|
10
|
Akher FB, Farrokhzadeh A, Ravenscroft N, Kuttel MM. Mechanistic Study of Potent Fluorinated EGFR Kinase Inhibitors with a Quinazoline Scaffold against L858R/T790M/C797S Resistance Mutation: Unveiling the Fluorine Substituent Cooperativity Effect on the Inhibitory Activity. J Phys Chem B 2020; 124:5813-5824. [PMID: 32603111 DOI: 10.1021/acs.jpcb.0c03440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorination has considerable potential with regard to the design of kinase inhibitors for anticarcinoma therapy. It was recently reported that fluorination increases the potency of inhibitors of the epidermal growth factor receptor (EGFR), mutations of which have been linked specifically to nonsmall-cell lung cancer. For the L858R/T790M/C797S triplet mutant (EGFRTM), a difluorinated inhibitor, 25g, was found to have 4.23 times greater potency against the EGFRTM than an unfluorinated inhibitor, 25a. This discovery necessitates a rational explanation for the underlying inhibitory mechanisms. Here, we apply multiple computational approaches to explore, validate, and differentiate the binding modes of 25a and 25g in the EGFRTM and investigate the cooperativity effect of fluorine substituents on the inhibitory activity. Our results showed that the EGFRTM in the presence of 25g undergoes a series of conformational changes that favor inhibitor binding to both the active and allosteric sites. Further, the cooperativity effect of fluorine substituents is positive: the complex stability is increased by each additional fluorine substituent. Estimated binding free energies show good correlation with the experimental biological activity. Subsequently, the decomposition energy analysis revealed that the van der Waals interaction is the principal force contributing to variations in the binding affinities of 25a and 25g to the EGFRTM. Per-residue energy-based hierarchical clustering analysis suggests that three hot-spot residues, L718, K745, and D855, are the key in achieving optimal binding modes for 25g with higher affinity in the EGFRTM compared to 25a. This study provides a rationale for the superior EGFRTM-inhibitory potency exhibited by 25g over 25a, which is expected to be useful for the future rational structure-based design of novel EGFRTM inhibitors with improved potency and selectivity.
Collapse
Affiliation(s)
- Farideh Badichi Akher
- Department of Computer Science, University of Cape Town, Cape Town 7701, South Africa.,Department of Chemistry, University of Cape Town, Cape Town 7700, South Africa
| | - Abdolkarim Farrokhzadeh
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Cape Town 7700, South Africa
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Cape Town 7701, South Africa
| |
Collapse
|
11
|
Fazio D, Criscuolo E, Piccoli A, Barboni B, Fezza F, Maccarrone M. Advances in the discovery of fatty acid amide hydrolase inhibitors: what does the future hold? Expert Opin Drug Discov 2020; 15:765-778. [PMID: 32292082 DOI: 10.1080/17460441.2020.1751118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Fatty acid amide hydrolase (FAAH) is a membrane-bound enzyme, that inactivates endogenous signaling lipids of the fatty acid amide family, including the endocannabinoid anandamide (N-arachidonoylethanolamine, AEA). The latter compound has been shown to regulate a number of important pathophysiological conditions in humans, like feeding, obesity, immune response, reproductive events, motor coordination, and neurological disorders. Hence, direct manipulation of the endocannabinoid tone is thought to have therapeutic potential. A new opportunity to develop effective drugs may arise from multi-target directed ligand (MTDL) strategies, which brings the concept that a single compound can recognize different targets involved in the cascade of pathophysiological events. AREAS COVERED This review reports the latest advances in the development of new single targeted and dual-targeted FAAH inhibitors over the past 5 years. EXPERT OPINION In recent years, several FAAH inhibitors have been synthesized and investigated, yet to date none of them has reached the market as a systemic drug. Due to the diligence of inherent redundancy and robustness in many biological networks and pathways, multitarget inhibitors present a new prospect in the pharmaceutical industry for treatment of complex diseases.
Collapse
Affiliation(s)
- Domenico Fazio
- Faculty of Biosciences and Technology for Food Agriculture and Environment, University of Teramo , Teramo, Italy.,European Center for Brain Research/IRCCS Santa Lucia Foundation , Rome, Italy
| | - Emanuele Criscuolo
- Department of Experimental Medicine, Tor Vergata University of Rome , Rome, Italy.,Department of Medicine, Campus Bio-Medico University of Rome , Rome, Italy
| | - Alessandra Piccoli
- Department of Medicine, Campus Bio-Medico University of Rome , Rome, Italy
| | - Barbara Barboni
- Faculty of Biosciences and Technology for Food Agriculture and Environment, University of Teramo , Teramo, Italy
| | - Filomena Fezza
- Department of Experimental Medicine, Tor Vergata University of Rome , Rome, Italy
| | - Mauro Maccarrone
- European Center for Brain Research/IRCCS Santa Lucia Foundation , Rome, Italy.,Department of Medicine, Campus Bio-Medico University of Rome , Rome, Italy
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Tripathi RKP. A perspective review on fatty acid amide hydrolase (FAAH) inhibitors as potential therapeutic agents. Eur J Med Chem 2019; 188:111953. [PMID: 31945644 DOI: 10.1016/j.ejmech.2019.111953] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 02/06/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is an important enzyme creditworthy of hydrolyzing endocannabinoids and related-amidated signalling lipids, discovery of which has pioneered novel arena of pharmacological canvasses to unwrap its curative potency in various diseased circumstances. It presents contemporary basis for understanding molecules regulating and mediating inflammatory reactions, pain, anxiety, depression, and neurodegeneration. FAAH inhibitors form vital approach for discovery of therapeutic agents that are concerned with local elevation of endocannabinoids under certain stimuli, debarring adverse/unwanted secondary effects from global activation of cannabinoid receptors by exogenous cannabimimetics. During past decades, several molecules with excellent potency developed through tailor-made approaches entered into clinical trials, but none could reach market. Hence, hunt for novel, non-toxic and selective FAAH inhibitors are on horizon. This review summarizes present perception on FAAH in conjunction with its structure, mechanism of catalysis and biological functions. It also foregrounds recent development of molecules belonging to diverse chemical classes as potential FAAH inhibitors bobbing up from in-depth chemical, mechanistic and computational studies published since 2015-November 2019, focusing on their potency. This review will assist readers to obtain rationale on FAAH as potential target for addressing various disease conditions, acquiring significant knowledge on recently established inhibitor scaffolds and their development potentials. New technologies including MD-MM simulations and 3D-QSAR studies allow mechanistic characterization of enzyme. Assessment of in-vitro and in-vivo efficacy of existing FAAH inhibitors will facilitate researchers to design novel ligands utilizing modern drug design methods. The discussions will also impose precaution in decision making process, quashing possibility of late stage failure.
Collapse
Affiliation(s)
- Rati Kailash Prasad Tripathi
- Department of Pharmaceutical Science, Sushruta School of Medical and Paramedical Sciences, Assam University (A Central University), Silchar, Assam, 788011, India; Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
| |
Collapse
|
14
|
Voice A, Tresadern G, van Vlijmen H, Mulholland A. Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors. J Chem Inf Model 2019; 59:4220-4227. [PMID: 31498988 DOI: 10.1021/acs.jcim.9b00404] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covalent inhibition has undergone a resurgence and is an important modern-day drug design and chemical biology approach. To avoid off-target interactions and to fine-tune reactivity, the ability to accurately predict reactivity is vitally important for the design and development of safer and more effective covalent drugs. Several ligand-only metrics have been proposed that promise quick and simple ways of determining covalent reactivity. In particular, we examine proton affinity and reaction energies calculated with the density functional B3LYP-D3/6-311+G**//B3LYP-D3/6-31G* method to assess the reactivity of a series of α,β-unsaturated carbonyl compounds that form covalent adducts with cysteine. We demonstrate that while these metrics correlate well with experiment for a diverse range of small reactive molecules these approaches fail for predicting the reactivity of drug-like compounds. We conclude that ligand-only metrics such as proton affinity and reaction energies do not capture determinants of reactivity in situ and fail to account for important factors such as conformation, solvation, and intermolecular interactions.
Collapse
Affiliation(s)
- Angus Voice
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , United Kingdom
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
| | - Adrian Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , United Kingdom
| |
Collapse
|
15
|
Akher FB, Farrokhzadeh A, Ravenscroft N, Kuttel MM. A Mechanistic Study of a Potent and Selective Epidermal Growth Factor Receptor Inhibitor against the L858R/T790M Resistance Mutation. Biochemistry 2019; 58:4246-4259. [PMID: 31589411 DOI: 10.1021/acs.biochem.9b00710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Covalent targeting is a promising strategy for increasing the potency and selectivity of potential drug candidates. This therapeutic approach was recently reported for the epidermal growth factor receptor (EGFR), wherein a covalent binder, 20g [N-(3-{7-[2-methoxy-4-(4-methylpiperazin-1-yl)phenylamino]-3,4-dihydro-3-isopropyl-2,4-dioxopyrimido[4,5-d]pyrimidin-1(2H)-yl}phenyl)acrylamide], demonstrated significant selectivity and inhibitory activity toward the EGFR L858R/T790M double mutant (EGFRDM) relative to the EGFR wild-type form (EGFRWT). The enhanced therapeutic potency of 20g against EGFRDM is 263 times greater than that against EGFRWT, which necessitates a rational explanation for the underlying selective and inhibitory mechanisms. In this work, we investigate the differential binding modes of 20g with EGFRWT and EGFRDM using molecular dynamics simulations coupled with free energy calculations and further identify key residues involved in the selective targeting, binding, and inhibitory mechanisms mediated by 20g. We find that systematic orientational and conformational changes in the α-loop, p-loop, active loop, and αC-helix are responsible for the disparate binding mechanisms and inhibitory prowess of 20g with respect to EGFRWT and EGFRDM. The calculated binding free energies show good correlation with the experimental biological activity. The total binding free energy difference between EGFRWT-20g and EGFRDM-20g is -11.47 kcal/mol, implying that 20g binds more strongly to EGFRDM. This enhanced binding affinity of 20g for EGFRDM is a result of a large increase in the van der Waals and electrostatic interactions with three critical residues (Met790, Gln791, and Met793) that are chiefly responsible for the high-affinity interactions mediated by 20g with EGFRDM relative to EGFRWT.
Collapse
Affiliation(s)
- Farideh Badichi Akher
- Department of Computer Science , University of Cape Town , Cape Town 7701 , South Africa.,Department of Chemistry , University of Cape Town , Cape Town 7701 , South Africa
| | - Abdolkarim Farrokhzadeh
- School of Chemistry and Physics , University of KwaZulu-Natal , Private Bag X01 , Pietermaritzburg 3209 , South Africa
| | - Neil Ravenscroft
- Department of Chemistry , University of Cape Town , Cape Town 7701 , South Africa
| | - Michelle M Kuttel
- Department of Computer Science , University of Cape Town , Cape Town 7701 , South Africa
| |
Collapse
|
16
|
Castelli R, Bozza N, Cavazzoni A, Bonelli M, Vacondio F, Ferlenghi F, Callegari D, Silva C, Rivara S, Lodola A, Digiacomo G, Fumarola C, Alfieri R, Petronini PG, Mor M. Balancing reactivity and antitumor activity: heteroarylthioacetamide derivatives as potent and time-dependent inhibitors of EGFR. Eur J Med Chem 2019; 162:507-524. [DOI: 10.1016/j.ejmech.2018.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023]
|
17
|
Kodani SD, Wan D, Wagner KM, Hwang SH, Morisseau C, Hammock BD. Design and Potency of Dual Soluble Epoxide Hydrolase/Fatty Acid Amide Hydrolase Inhibitors. ACS OMEGA 2018; 3:14076-14086. [PMID: 30411058 PMCID: PMC6210075 DOI: 10.1021/acsomega.8b01625] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is responsible for regulating concentrations of the endocannabinoid arachidonoyl ethanolamide. Multiple FAAH inhibitors have been developed for clinical trials and have failed to demonstrate efficacy at treating pain, despite promising preclinical data. One approach toward increasing the efficacy of FAAH inhibitors is to concurrently inhibit other targets responsible for regulating pain. Here, we designed dual inhibitors targeting the enzymes FAAH and soluble epoxide hydrolase (sEH), which are targets previously shown to synergize at reducing inflammatory and neuropathic pain. Exploration of the sEH/FAAH inhibitor structure-activity relationship started with PF-750, a FAAH inhibitor (IC50 = 19 nM) that weakly inhibited sEH (IC50 = 640 nM). Potency was optimized resulting in an inhibitor with improved potency on both targets (11, sEH IC50 = 5 nM, FAAH IC50 = 8 nM). This inhibitor demonstrated good target selectivity, pharmacokinetic properties (AUC = 1200 h nM, t 1/2 = 4.9 h in mice), and in vivo target engagement.
Collapse
|
18
|
Saha A, Shih AY, Mirzadegan T, Seierstad M. Predicting the Binding of Fatty Acid Amide Hydrolase Inhibitors by Free Energy Perturbation. J Chem Theory Comput 2018; 14:5815-5822. [PMID: 30289722 DOI: 10.1021/acs.jctc.8b00672] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since a goal of most drug discovery projects in either academia or industry is to design molecules that selectively bind to the desired protein, determination of protein-ligand binding free energies is of utmost importance in computer aided drug design. With the help of significant improvements in computer power, enhanced sampling techniques and accuracy of force fields, FEP (free energy perturbation) is becoming an important tool to estimate binding free energies in many drug discovery projects both retrospectively and prospectively. We have evaluated the ability of Schrödinger's FEP+ to predict relative binding free energies of a congeneric series of noncovalent fatty acid amide hydrolase (FAAH) inhibitors using an in-house crystal structure. This study shows that although an impressively accurate correlation can be obtained with experimental IC50s considering small perturbations on the deeper side of the pocket, the same was not observed with small perturbations on the relatively more open-ended and solvent-accessible side of the pocket. To understand these observations, we thoroughly investigated several key factors including the sampling of asymmetrically substituted rings, different perturbation maps, impact of simultaneous perturbations at two different ends of the ligand, and selecting the perturbations in a "chemically sensible" way.
Collapse
Affiliation(s)
- Arjun Saha
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
| | - Amy Y Shih
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
| | - Taraneh Mirzadegan
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
| | - Mark Seierstad
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
| |
Collapse
|
19
|
Lodola A, Bertolini S, Biagetti M, Capacchi S, Facchinetti F, Gallo PM, Pappani A, Mor M, Pala D, Rivara S, Visentini F, Corsi M, Capelli AM. Atropisomerism and Conformational Equilibria: Impact on PI3Kδ Inhibition of 2-((6-Amino-9H-purin-9-yl)methyl)-5-methyl-3-(o-tolyl)quinazolin-4(3H)-one (IC87114) and Its Conformationally Restricted Analogs. J Med Chem 2017; 60:4304-4315. [DOI: 10.1021/acs.jmedchem.7b00247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | - Serena Bertolini
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Matteo Biagetti
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Silvia Capacchi
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Fabrizio Facchinetti
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Paola Maria Gallo
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Alice Pappani
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Marco Mor
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | - Daniele Pala
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | | | - Mauro Corsi
- Aptuit s.r.l., Via Fleming 4, 37135 Verona, Italy
| | - Anna Maria Capelli
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| |
Collapse
|
20
|
Sunduru N, Svensson M, Cipriano M, Marwaha S, Andersson CD, Svensson R, Fowler CJ, Elofsson M. N-aryl 2-aryloxyacetamides as a new class of fatty acid amide hydrolase (FAAH) inhibitors. J Enzyme Inhib Med Chem 2017; 32:513-521. [PMID: 28114819 PMCID: PMC6009913 DOI: 10.1080/14756366.2016.1265520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fatty acid amide hydrolase (FAAH) is a promising target for the development of drugs to treat neurological diseases. In search of new FAAH inhibitors, we identified 2-(4-cyclohexylphenoxy)-N-(3-(oxazolo[4,5-b]pyridin-2-yl)phenyl)acetamide, 4g, with an IC50 of 2.6 µM as a chemical starting point for the development of potent FAAH inhibitors. Preliminary hit-to-lead optimisation resulted in 2-(4-phenylphenoxy)-N-(3-(oxazolo[4,5-b]pyridin-2-yl)phenyl)acetamide, 4i, with an IC50 of 0.35 µM.
Collapse
Affiliation(s)
- Naresh Sunduru
- a Department of Chemistry , Umeå University , Umeå , Sweden
| | - Mona Svensson
- b Department of Pharmacology and Clinical Neuroscience , Umeå University , Umeå , Sweden
| | - Mariateresa Cipriano
- b Department of Pharmacology and Clinical Neuroscience , Umeå University , Umeå , Sweden
| | - Sania Marwaha
- a Department of Chemistry , Umeå University , Umeå , Sweden
| | | | - Richard Svensson
- c Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling platform (UDOPP) , Uppsala University , Uppsala , Sweden
| | - Christopher J Fowler
- b Department of Pharmacology and Clinical Neuroscience , Umeå University , Umeå , Sweden
| | | |
Collapse
|
21
|
Lodola A, Castelli R, Mor M, Rivara S. Fatty acid amide hydrolase inhibitors: a patent review (2009-2014). Expert Opin Ther Pat 2015; 25:1247-66. [PMID: 26413912 DOI: 10.1517/13543776.2015.1067683] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Fatty acid amide hydrolase (FAAH) is a key enzyme responsible for the degradation of the endocannabinoid anandamide. FAAH inactivation is emerging as a strategy to treat several CNS and peripheral diseases, including inflammation and pain. The search for effective FAAH inhibitors has thus become a key focus in present drug discovery. AREAS COVERED Patents and patent applications published from 2009 to 2014 in which novel chemical classes are claimed to inhibit FAAH. EXPERT OPINION FAAH is a promising target for treating many disease conditions including pain, inflammation and mood disorders. In the last few years, remarkable efforts have been made to develop new FAAH inhibitors (either reversible and irreversible) characterized by excellent potency and selectivity, to complete the arsenal of tools for modulating FAAH activity. The failure of PF-04457845 in a Phase II study on osteoarthritis pain has not flattened the interest in FAAH inhibitors. New clinical trials on 'classical' FAAH inhibitors are now ongoing, and new strategies based on compounds with peculiar in vivo distribution (e.g., peripheral) or with multiple pharmacological activities (e.g., FAAH and COX) are under investigation and could boost the therapeutic potential of this class in the next future.
Collapse
Affiliation(s)
- Alessio Lodola
- a 1 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy
| | - Riccardo Castelli
- b 2 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy
| | - Marco Mor
- c 3 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy +39 0521 905059 ; +39 0521 905006 ;
| | - Silvia Rivara
- a 1 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy
| |
Collapse
|
22
|
Palermo G, Bauer I, Campomanes P, Cavalli A, Armirotti A, Girotto S, Rothlisberger U, De Vivo M. Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets. PLoS Comput Biol 2015; 11:e1004231. [PMID: 26111155 PMCID: PMC4481349 DOI: 10.1371/journal.pcbi.1004231] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/09/2015] [Indexed: 12/31/2022] Open
Abstract
The fatty acid amide hydrolase (FAAH) regulates the endocannabinoid system cleaving primarily the lipid messenger anandamide. FAAH has been well characterized over the years and, importantly, it represents a promising drug target to treat several diseases, including inflammatory-related diseases and cancer. But its enzymatic mechanism for lipid selection to specifically hydrolyze anandamide, rather than similar bioactive lipids, remains elusive. Here, we clarify this mechanism in FAAH, examining the role of the dynamic paddle, which is formed by the gating residues Phe432 and Trp531 at the boundary between two cavities that form the FAAH catalytic site (the “membrane-access” and the “acyl chain-binding” pockets). We integrate microsecond-long MD simulations of wild type and double mutant model systems (Phe432Ala and Trp531Ala) of FAAH, embedded in a realistic membrane/water environment, with mutagenesis and kinetic experiments. We comparatively analyze three fatty acid substrates with different hydrolysis rates (anandamide > oleamide > palmitoylethanolamide). Our findings identify FAAH’s mechanism to selectively accommodate anandamide into a multi-pocket binding site, and to properly orient the substrate in pre-reactive conformations for efficient hydrolysis that is interceded by the dynamic paddle. Our findings therefore endorse a structural framework for a lipid selection mechanism mediated by structural flexibility and gating residues between multiple binding cavities, as found in FAAH. Based on the available structural data, this exquisite catalytic strategy for substrate specificity seems to be shared by other lipid-degrading enzymes with similar enzymatic architecture. The mechanistic insights for lipid selection might assist de-novo enzyme design or drug discovery efforts. We describe a new structural enzymatic framework to regulate substrate specificity in lipid-degrading enzymes such as fatty acid amide hydrolase (FAAH), a key enzyme for the endocannabinoid lipid signaling that hydrolyzes a variety of lipids, however with different catalytic rates. The identified novel mechanism and key features for lipid selection in FAAH are then analysed in the context of other relevant lipid-degrading enzymes. Through the integration of microsecond-long molecular dynamics simulations with mutagenesis and kinetic experiments, our study suggests that structural flexibility, gating residues and multiple cavities in one catalytic site are keys to lipid selection in the endocannabinoid system. Our results suggest that the structural framework proposed here could likely be a general enzymatic strategy of other lipid-degrading enzymes to select the preferred lipid substrate within a broad spectrum of biologically active lipids. This new, and likely general, structural framework for lipid selection in FAAH could therefore now encourage additional experimental verifications of the role of ligand and structural flexibility, as regulated by key gating residues at the boundaries of multiple cavities forming a single catalytic site, as observed in several other lipid-degrading enzymes.
Collapse
Affiliation(s)
- Giulia Palermo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Genova, Italy
| | - Inga Bauer
- CompuNet, Istituto Italiano di Tecnologia, Genova, Italy
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Andrea Armirotti
- D3-PharmaChemistry, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Genova, Italy
- * E-mail:
| |
Collapse
|
23
|
Aghazadeh Tabrizi M, Baraldi PG, Ruggiero E, Saponaro G, Baraldi S, Romagnoli R, Martinelli A, Tuccinardi T. Pyrazole phenylcyclohexylcarbamates as inhibitors of human fatty acid amide hydrolases (FAAH). Eur J Med Chem 2015; 97:289-305. [DOI: 10.1016/j.ejmech.2015.04.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Giedroyć-Piasecka W, Dyguda-Kazimierowicz E, Beker W, Mor M, Lodola A, Sokalski WA. Physical Nature of Fatty Acid Amide Hydrolase Interactions with Its Inhibitors: Testing a Simple Nonempirical Scoring Model. J Phys Chem B 2014; 118:14727-36. [PMID: 25420234 DOI: 10.1021/jp5059287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is an enzyme responsible for the deactivating hydrolysis of fatty acid ethanolamide neuromodulators. FAAH inhibitors have gained considerable interest due to their possible application in the treatment of anxiety, inflammation, and pain. In the context of inhibitor design, the availability of reliable computational tools for predicting binding affinity is still a challenging task, and it is now well understood that empirical scoring functions have several limitations that in principle could be overcome by quantum mechanics. Herein, systematic ab initio analyses of FAAH interactions with a series of inhibitors belonging to the class of the N-alkylcarbamic acid aryl esters have been performed. In contrast to our earlier studies of other classes of enzyme-inhibitor complexes, reasonable correlation with experimental results required us to consider correlation effects along with electrostatic term. Therefore, the simplest comprehensive nonempirical model allowing for qualitative predictions of binding affinities for FAAH ligands consists of electrostatic multipole and second-order dispersion terms. Such a model has been validated against the relative stabilities of the benchmark S66 set of biomolecular complexes. As it does not involve parameters fitted to experimentally derived data, this model offers a unique opportunity for generally applicable inhibitor design and virtual screening.
Collapse
Affiliation(s)
| | | | - Wiktor Beker
- Department of Chemistry, Wrocław University of Technology , Wrocław, Poland
| | - Marco Mor
- Pharmacy Department, Università di Parma , Parma, Italy
| | | | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Technology , Wrocław, Poland
| |
Collapse
|
26
|
Colombano G, Albani C, Ottonello G, Ribeiro A, Scarpelli R, Tarozzo G, Daglian J, Jung KM, Piomelli D, Bandiera T. O-(triazolyl)methyl carbamates as a novel and potent class of fatty acid amide hydrolase (FAAH) inhibitors. ChemMedChem 2014; 10:380-95. [PMID: 25338703 DOI: 10.1002/cmdc.201402374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 11/09/2022]
Abstract
Inhibition of fatty acid amide hydrolase (FAAH) activity is under investigation as a valuable strategy for the treatment of several disorders, including pain and drug addiction. A number of potent FAAH inhibitors belonging to different chemical classes have been disclosed to date; O-aryl carbamates are one of the most representative families. In the search for novel FAAH inhibitors, a series of O-(1,2,3-triazol-4-yl)methyl carbamate derivatives were designed and synthesized exploiting a copper- catalyzed [3+2] cycloaddition reaction between azides and alkynes (click chemistry). Exploration of the structure-activity relationships within this new class of compounds identified potent inhibitors of both rat and human FAAH with IC50 values in the single-digit nanomolar range. In addition, these derivatives showed improved stability in rat plasma and kinetic solubility in buffer with respect to the lead compound. Based on the results of the study, the novel analogues identified can be considered to be promising starting point for the development of new FAAH inhibitors with improved drug-like properties.
Collapse
Affiliation(s)
- Giampiero Colombano
- Drug Discovery & Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova (Italy); The Institute of Cancer Research, 15 Cotswold Rd, Sutton, Surrey SM2 5NG (UK). ,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
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
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
Hou Q, Sheng X, Liu Y. QM/MM studies of the mechanism of unusual bifunctional fructose-1,6-bisphosphate aldolase/phosphatase. Phys Chem Chem Phys 2014; 16:11366-73. [DOI: 10.1039/c3cp55263b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
30
|
Patel JZ, Parkkari T, Laitinen T, Kaczor AA, Saario SM, Savinainen JR, Navia-Paldanius D, Cipriano M, Leppänen J, Koshevoy IO, Poso A, Fowler CJ, Laitinen JT, Nevalainen T. Chiral 1,3,4-oxadiazol-2-ones as highly selective FAAH inhibitors. J Med Chem 2013; 56:8484-96. [PMID: 24083878 DOI: 10.1021/jm400923s] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present study, identification of chiral 1,3,4-oxadiazol-2-ones as potent and selective FAAH inhibitors has been described. The separated enantiomers showed clear differences in the potency and selectivity toward both FAAH and MAGL. Additionally, the importance of the chirality on the inhibitory activity and selectivity was proven by the simplification approach by removing a methyl group at the 3-position of the 1,3,4-oxadiazol-2-one ring. The most potent compound of the series, the S-enantiomer of 3-(1-(4-isobutylphenyl)ethyl)-5-methoxy-1,3,4-oxadiazol-2(3H)-one (JZP-327A, 51), inhibited human recombinant FAAH (hrFAAH) in the low nanomolar range (IC50 = 11 nM), whereas its corresponding R-enantiomer 52 showed only moderate inhibition toward hrFAAH (IC50 = 0.24 μM). In contrast to hrFAAH, R-enantiomer 52 was more potent in inhibiting the activity of hrMAGL compared to S-enantiomer 51 (IC50 = 4.0 μM and 16% inhibition at 10 μM, respectively). The FAAH selectivity of the compound 51 over the supposed main off-targets, MAGL and COX, was found to be >900-fold. In addition, activity-based protein profiling (ABPP) indicated high selectivity over other serine hydrolases. Finally, the selected S-enantiomers 51, 53, and 55 were shown to be tight binding, slowly reversible inhibitors of the hrFAAH.
Collapse
Affiliation(s)
- Jayendra Z Patel
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , P.O. Box 1627, FIN-70211 Kuopio, Finland
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|