1
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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Dangat Y, Freindorf M, Kraka E. Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study. J Am Chem Soc 2024; 146:145-158. [PMID: 38055807 DOI: 10.1021/jacs.3c06397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.
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Affiliation(s)
- Yuvraj Dangat
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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3
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Blunt NS, Camps J, Crawford O, Izsák R, Leontica S, Mirani A, Moylett AE, Scivier SA, Sünderhauf C, Schopf P, Taylor JM, Holzmann N. Perspective on the Current State-of-the-Art of Quantum Computing for Drug Discovery Applications. J Chem Theory Comput 2022; 18:7001-7023. [PMID: 36355616 DOI: 10.1021/acs.jctc.2c00574] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Computational chemistry is an essential tool in the pharmaceutical industry. Quantum computing is a fast evolving technology that promises to completely shift the computational capabilities in many areas of chemical research by bringing into reach currently impossible calculations. This perspective illustrates the near-future applicability of quantum computation of molecules to pharmaceutical problems. We briefly summarize and compare the scaling properties of state-of-the-art quantum algorithms and provide novel estimates of the quantum computational cost of simulating progressively larger embedding regions of a pharmaceutically relevant covalent protein-drug complex involving the drug Ibrutinib. Carrying out these calculations requires an error-corrected quantum architecture that we describe. Our estimates showcase that recent developments on quantum phase estimation algorithms have dramatically reduced the quantum resources needed to run fully quantum calculations in active spaces of around 50 orbitals and electrons, from estimated over 1000 years using the Trotterization approach to just a few days with sparse qubitization, painting a picture of fast and exciting progress in this nascent field.
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Affiliation(s)
- Nick S Blunt
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Joan Camps
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Ophelia Crawford
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Róbert Izsák
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Sebastian Leontica
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Arjun Mirani
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Alexandra E Moylett
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Sam A Scivier
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Christoph Sünderhauf
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Patrick Schopf
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Jacob M Taylor
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Nicole Holzmann
- Riverlane, St. Andrews House, 59 St. Andrews Street, Cambridge CB2 3BZ, United Kingdom.,Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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4
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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.
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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
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5
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Rocha JF, Sousa SF, Cerqueira NMFSA. Computational Studies Devoted to the Catalytic Mechanism of Threonine Aldolase, a Critical Enzyme in the Pharmaceutical Industry to Synthesize β-Hydroxy-α-amino Acids. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Juliana F. Rocha
- Associate Laboratory i4HB − Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO─Applied Molecular Biosciences Unit, BioSIM─Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- Associate Laboratory i4HB − Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO─Applied Molecular Biosciences Unit, BioSIM─Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Nuno M. F. Sousa A. Cerqueira
- Associate Laboratory i4HB − Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO─Applied Molecular Biosciences Unit, BioSIM─Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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6
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Bím D, Navrátil M, Gutten O, Konvalinka J, Kutil Z, Culka M, Navrátil V, Alexandrova AN, Bařinka C, Rulíšek L. Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II. J Phys Chem B 2022; 126:132-143. [PMID: 34978450 DOI: 10.1021/acs.jpcb.1c09240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol-1 can be inferred for the known kcat ≈ 1 s-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (kcat = 8.6 × 10-5 s-1 to 2.7 s-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.
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Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 2120 00 Prague, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Václav Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
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7
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Jerves C, Neves RPP, Ramos MJ, da Silva S, Fernandes PA. Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03700] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Carola Jerves
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
- Facultad de Ciencias Químicas, Universidad de Cuenca, Av. 12 de Abril y Av. Loja, Cuenca 010202, Ecuador
| | - Rui P. P. Neves
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Saulo da Silva
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
- Facultad de Ciencias Químicas, Universidad de Cuenca, Av. 12 de Abril y Av. Loja, Cuenca 010202, Ecuador
| | - Pedro A. Fernandes
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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8
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Lou XF, Du YZ, Xu XL. Endogenous Enzyme-responsive Nanoplatforms for Anti-tumor Therapy. Curr Drug Targets 2021; 22:845-855. [PMID: 33459230 DOI: 10.2174/1389450122666210114095614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 11/22/2022]
Abstract
The emergency of responsive drug delivery systems has contributed to reduced cytotoxicity, improved permeability in tissues and extended circulation time of the active drug. In particular, enzyme-responsive nanoplatforms have attracted a lot of attention due to the specificity and efficiency of an enzyme-catalyzed reaction. In this review, enzyme-based mono responsive drug delivery systems designed in the past 5 years have been summarized. These drug delivery systems were introduced by different tumor-related enzymes such as matrix metalloproteinase, esterase, hyaluronidase, caspase and cathepsin. Moreover, the enzyme-sensitive nanoplatforms activated by dual-stimuli have been also described. Although great progress had been made in the past years, the translation into clinical practice is still difficult. Thus, three obstacles (enzyme heterogeneity, reaction environment, animal model) were also discussed. In short, enzyme-activated drug delivery systems offer great potential in treating cancers.
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Affiliation(s)
- Xue-Fang Lou
- School of Medicine, Zhejiang University City College, 51 Hu-Zhou Street, Hangzhou 310015, China
| | - Yong-Zhong Du
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Ling Xu
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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9
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Silva Teixeira CS, Sousa SF, Cerqueira NMFSA. An Unsual Cys-Glu-Lys Catalytic Triad is Responsible for the Catalytic Mechanism of the Nitrilase Superfamily: A QM/MM Study on Nit2. Chemphyschem 2021; 22:796-804. [PMID: 33463886 DOI: 10.1002/cphc.202000751] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/13/2021] [Indexed: 12/29/2022]
Abstract
Nitrilase 2 (Nit2) is a representative member of the nitrilase superfamily that catalyzes the hydrolysis of α-ketosuccinamate into oxaloacetate. It has been associated with the metabolism of rapidly dividing cells like cancer cells. The catalytic mechanism of Nit2 employs a catalytic triad formed by Cys191, Glu81 and Lys150. The Cys191 and Glu81 play an active role during the catalytic process while the Lys150 is shown to play only a secondary role. The results demonstrate that the catalytic mechanism of Nit2 involves four steps. The nucleophilic attack of Cys191 to the α-ketosuccinamate, the formation of two tetrahedral enzyme adducts and the hydrolysis of a thioacyl-enzyme intermediate, from which results the formation of oxaloacetate and enzymatic turnover. The rate limiting step of the catalytic process is the formation of the first tetrahedral intermediate with a calculated activation free energy of 18.4 kcal/mol, which agrees very well with the experimental kcat (17.67 kcal/mol).
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Affiliation(s)
- Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
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10
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Ribeiro PMG, Fernandes HS, Maia LB, Sousa SF, Moura JJG, Cerqueira NMFSA. The complete catalytic mechanism of xanthine oxidase: a computational study. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01029d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this article, quantum mechanical/molecular mechanical (QM/MM) methods were used to study the full catalytic mechanism of xanthine oxidase (XO).
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Affiliation(s)
- Pedro M. G. Ribeiro
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - Henrique S. Fernandes
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - Luísa B. Maia
- LAQV
- REQUIMTE
- NOVA School of Science and Technology
- Campus de Caparica
- 2829-516 Caparica
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - José J. G. Moura
- LAQV
- REQUIMTE
- NOVA School of Science and Technology
- Campus de Caparica
- 2829-516 Caparica
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
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11
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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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12
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Freitas DS, Sousa CEA, Parente J, Drogalin A, Gil Fortes A, Cerqueira NMFSA, Alves MJ. (3S,4R)-3,4-Dihydroxy-N-alkyl-l-homoprolines: synthesis and computational mechanistic studies. Org Biomol Chem 2019; 17:10052-10064. [PMID: 31748775 DOI: 10.1039/c9ob02141h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is the first synthetic report of (3S,4R)-dihydroxy-N-alkyl-l-homoprolines described so far. 2,4-O-Benzylidene-d-erythrose was obtained from d-glucose with an improved yield, and then transformed into the title (3S,4R)-dihydroxy-N-alkyl-l-homoprolines, in a two-step strategy, with excellent overall yields. Hydrogenolysis of the benzyl group led to the NH congener. The synthesis of final products from 1,4-lactone intermediates was studied by computational means either under acidic or basic conditions. The theoretical mechanism studies fully explain the experimental results: (a) an equilibrium between l-homoprolines and their bicyclic counterparts is established in acids; (b) the equilibrium suffers a complete displacement towards the l-homoproline side in a basic medium.
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Affiliation(s)
- David S Freitas
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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13
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Teixeira CSS, Ramos MJ, Sousa SF, Cerqueira NMFSA. Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carla S. Silva Teixeira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTEDepartamento de Química e BioquímicaFaculdade de CiênciasUniversidade do Porto Porto 4169-007 Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
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14
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Calixto AR, Ramos MJ, Fernandes PA. Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway. Chem Sci 2019; 10:7212-7221. [PMID: 31588289 PMCID: PMC6677113 DOI: 10.1039/c9sc01464k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/10/2019] [Indexed: 02/04/2023] Open
Abstract
The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes' catalytic power. Following this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction lead to the lowest activation barriers that mostly contribute to the macroscopically observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of the HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme's chemistry: they influence the barrier height, something also observed in the past in other enzymes, and they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the "one enzyme-one substrate-one reaction mechanism" paradigm. Two different reaction mechanisms, with similar reactant probabilities and barrier heights, lead to the same gem-diol intermediate. Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder. The results make us realize the unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.
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Affiliation(s)
- Ana Rita Calixto
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Maria João Ramos
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Pedro Alexandrino Fernandes
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
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15
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Rocha JF, Pina AF, Sousa SF, Cerqueira NMFSA. PLP-dependent enzymes as important biocatalysts for the pharmaceutical, chemical and food industries: a structural and mechanistic perspective. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01210a] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PLP-dependent enzymes described on this review are attractive targets for enzyme engineering towards their application in an industrial biotechnology framework.
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Affiliation(s)
- Juliana F. Rocha
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
| | - André F. Pina
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
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16
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Wei WJ, Qian HX, Wang WJ, Liao RZ. Computational Understanding of the Selectivities in Metalloenzymes. Front Chem 2018; 6:638. [PMID: 30622942 PMCID: PMC6308299 DOI: 10.3389/fchem.2018.00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/07/2018] [Indexed: 01/26/2023] Open
Abstract
Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.
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Affiliation(s)
| | | | | | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, China
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17
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Fernandes HS, Ramos MJ, Cerqueira NMFSA. Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02321] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Henrique S. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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18
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Rocha JF, Freitas DS, Noro J, Silva Teixeira CS, Sousa CEA, Alves MJ, Cerqueira NMFSA. Total Stereoselective Michael Addition of N- and S- Nucleophiles to a d-Erythrosyl 1,5-Lactone Derivative. Experimental and Theoretical Studies Devoted to the Synthesis of 2,6-Dideoxy-4-functionalized-d- ribono-hexono-1,4-lactone. J Org Chem 2018; 83:8011-8019. [PMID: 29924603 DOI: 10.1021/acs.joc.8b00769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of a 1,5-lactone 2,4- O-alkylidene-d-erythrose derivative was found to be a highly stereoselective template in Michael addition trough the reaction of a d-erythrosyl 1,5-lactone derivative with nitrogen and sulfur nucleophiles. The sulfur adducts formed are 1 (d-erythrose derivative):1 (nucleophile), and the nitrogen adducts are 1:2. Both were then treated under HCl to give 2,6-dideoxy-4-functionalized-d- ribono-hexono-1,4-lactone by a reaction cascade in high overall yield. Reaction's scale up even improves the yield. The theoretical and computational results clearly explain the origin of the stereoselectivity, and the energetic course of reactions starting with nitrogen and sulfide nucleophiles. Considering that the 1,4-lactones obtained in this work offer a new molecular scaffold for organic synthesis, these new results provide a solid theoretical platform that can be used to speed up synthesis of other derivatives in a stereo- and regioselective way.
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Affiliation(s)
- Juliana F Rocha
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal
| | - David S Freitas
- Departamento de Química , Universidade do Minho , Campus de Gualtar , 4710-057 Braga , Portugal
| | - Jennifer Noro
- Departamento de Química , Universidade do Minho , Campus de Gualtar , 4710-057 Braga , Portugal
| | - Carla S Silva Teixeira
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal
| | - Cristina E A Sousa
- Departamento de Química , Universidade do Minho , Campus de Gualtar , 4710-057 Braga , Portugal
| | - Maria J Alves
- Departamento de Química , Universidade do Minho , Campus de Gualtar , 4710-057 Braga , Portugal
| | - Nuno M F S A Cerqueira
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal
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