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Raghavan B, Paulikat M, Ahmad K, Callea L, Rizzi A, Ippoliti E, Mandelli D, Bonati L, De Vivo M, Carloni P. Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations. J Chem Inf Model 2023; 63:3647-3658. [PMID: 37319347 PMCID: PMC10302481 DOI: 10.1021/acs.jcim.3c00557] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Indexed: 06/17/2023]
Abstract
The initial phases of drug discovery - in silico drug design - could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines - so far an unmet and crucial goal - will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC-QM/MM MD simulations with parallel efficiency of ∼70% up to >80,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate toward exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers.
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Affiliation(s)
- Bharath Raghavan
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
- Department
of Physics, RWTH Aachen University, Aachen 52074, Germany
| | - Mirko Paulikat
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
| | - Katya Ahmad
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
| | - Lara Callea
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Andrea Rizzi
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
- Atomistic
Simulations, Italian Institute of Technology, Genova 16163, Italy
| | - Emiliano Ippoliti
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
| | - Davide Mandelli
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
| | - Laura Bonati
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Marco De Vivo
- Molecular
Modelling and Drug Discovery, Italian Institute
of Technology, Genova 16163, Italy
| | - Paolo Carloni
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, Jülich 52428, Germany
- Department
of Physics and Universitätsklinikum, RWTH Aachen University, Aachen 52074, Germany
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Hassanzadeh P. Towards the quantum-enabled technologies for development of drugs or delivery systems. J Control Release 2020; 324:260-279. [DOI: 10.1016/j.jconrel.2020.04.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]
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Amaro RE, Mulholland AJ. Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. Nat Rev Chem 2018; 2:0148. [PMID: 30949587 PMCID: PMC6445369 DOI: 10.1038/s41570-018-0148] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Drug action is inherently multiscale: it connects molecular interactions to emergent properties at cellular and larger scales. Simulation techniques at each of these different scales are already central to drug design and development, but methods capable of connecting across these scales will extend understanding of complex mechanisms and the ability to predict biological effects. Improved algorithms, ever-more-powerful computing architectures and the accelerating growth of rich datasets are driving advances in multiscale modeling methods capable of bridging chemical and biological complexity from the atom to the cell. Particularly exciting is the development of highly detailed, structure-based, physical simulations of biochemical systems, which are now able to access experimentally relevant timescales for large systems and, at the same time, achieve unprecedented accuracy. In this Perspective, we discuss how emerging data-rich, physics-based multiscale approaches are of the cusp of realizing long-promised impact in the discovery, design and development of novel therapeutics. We highlight emerging methods and applications in this growing field, and outline how different scales can be combined in practical modelling and simulation strategies.
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Affiliation(s)
- Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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Yang Y, Pan L, Lightstone F, Merz K. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis. Methods Enzymol 2016; 577:1-29. [DOI: 10.1016/bs.mie.2016.05.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
CONSPECTUS: The role dynamics plays in proteins is of intense contemporary interest. Fundamental insights into how dynamics affects reactivity and product distributions will facilitate the design of novel catalysts that can produce high quality compounds that can be employed, for example, as fuels and life saving drugs. We have used molecular dynamics (MD) methods and combined quantum mechanical/molecular mechanical (QM/MM) methods to study a series of proteins either whose substrates are too far away from the catalytic center or whose experimentally resolved substrate binding modes cannot explain the observed product distribution. In particular, we describe studies of farnesyl transferase (FTase) where the farnesyl pyrophosphate (FPP) substrate is ∼8 Å from the zinc-bound peptide in the active site of FTase. Using MD and QM/MM studies, we explain how the FPP substrate spans the gulf between it and the active site, and we have elucidated the nature of the transition state (TS) and offered an alternate explanation of experimentally observed kinetic isotope effects (KIEs). Our second story focuses on the nature of substrate dynamics in the aromatic prenyltransferase (APTase) protein NphB and how substrate dynamics affects the observed product distribution. Through the examples chosen we show the power of MD and QM/MM methods to provide unique insights into how protein substrate dynamics affects catalytic efficiency. We also illustrate how complex these reactions are and highlight the challenges faced when attempting to design de novo catalysts. While the methods used in our previous studies provided useful insights, several clear challenges still remain. In particular, we have utilized a semiempirical QM model (self-consistent charge density functional tight binding, SCC-DFTB) in our QM/MM studies since the problems we were addressing required extensive sampling. For the problems illustrated, this approach performed admirably (we estimate for these systems an uncertainty of ∼2 kcal/mol), but it is still a semiempirical model, and studies of this type would benefit greatly from more accurate ab initio or DFT models. However, the challenge with these methods is to reach the level of sampling needed to study systems where large conformational changes happen in the many nanoseconds to microsecond time regimes. Hence, how to couple expensive and accurate QM methods with sophisticated sampling algorithms is an important future challenge especially when large-scale studies of catalyst design become of interest. The use of MD and QM/MM models to elucidate enzyme catalytic pathways and to design novel catalytic agents is in its infancy but shows tremendous promise. While this Account summarizes where we have been, we also discuss briefly future directions that improve our fundamental ability to understand enzyme catalysis.
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Affiliation(s)
- Dhruva K. Chakravorty
- Department of Chemistry, 2000 Lakeshore Drive, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Kenneth M. Merz
- Department of Chemistry and the Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing Michigan 48824-1322, United States
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Palsuledesai CC, Distefano MD. Protein prenylation: enzymes, therapeutics, and biotechnology applications. ACS Chem Biol 2015; 10:51-62. [PMID: 25402849 PMCID: PMC4301080 DOI: 10.1021/cb500791f] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Protein
prenylation is a ubiquitous covalent post-translational modification
found in all eukaryotic cells, comprising attachment of either a farnesyl
or a geranylgeranyl isoprenoid. It is essential for the proper cellular
activity of numerous proteins, including Ras family GTPases and heterotrimeric
G-proteins. Inhibition of prenylation has been extensively investigated
to suppress the activity of oncogenic Ras proteins to achieve antitumor
activity. Here, we review the biochemistry of the prenyltransferase
enzymes and numerous isoprenoid analogs synthesized to investigate
various aspects of prenylation and prenyltransferases. We also give
an account of the current status of prenyltransferase inhibitors as
potential therapeutics against several diseases including cancers,
progeria, aging, parasitic diseases, and bacterial and viral infections.
Finally, we discuss recent progress in utilizing protein prenylation
for site-specific protein labeling for various biotechnology applications.
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Affiliation(s)
- Charuta C. Palsuledesai
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Shen M, Pan P, Li Y, Li D, Yu H, Hou T. Farnesyltransferase and geranylgeranyltransferase I: structures, mechanism, inhibitors and molecular modeling. Drug Discov Today 2014; 20:267-76. [PMID: 25450772 DOI: 10.1016/j.drudis.2014.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/13/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022]
Abstract
Farnesyltransferase (FTase) and geranylgeranyltransferase type I (GGTase-I) have crucial roles in the post-translational modifications of Ras proteins and, therefore, they are promising therapeutic targets for the treatment of various Ras-induced cancers and several other kinds of diseases. In this review, we provide an overview of the structures and biological functions of FTase and GGTase-I. Then, we summarize the typical inhibitors of FTase and GGTase-I, and highlight the drug candidates in clinical trials. In addition, we survey some recent advances in computer-aided drug design (CADD) and molecular modeling studies of FTase and GGTase-I.
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Affiliation(s)
- Mingyun Shen
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Peichen Pan
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huidong Yu
- Crystal Pharmatech, 707 Alexander Road Building 2, Suite 208, Princeton, NJ 08540, USA.
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Palermo G, Rothlisberger U, Cavalli A, De Vivo M. Computational insights into function and inhibition of fatty acid amide hydrolase. Eur J Med Chem 2014; 91:15-26. [PMID: 25240419 DOI: 10.1016/j.ejmech.2014.09.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/01/2014] [Accepted: 09/11/2014] [Indexed: 01/11/2023]
Abstract
The Fatty Acid Amide Hydrolase (FAAH) enzyme is a membrane-bound serine hydrolase responsible for the deactivating hydrolysis of a family of naturally occurring fatty acid amides. FAAH is a critical enzyme of the endocannabinoid system, being mainly responsible for regulating the level of its main cannabinoid substrate anandamide. For this reason, pharmacological inhibition of FAAH, which increases the level of endogenous anandamide, is a promising strategy to cure a variety of diseases including pain, inflammation, and cancer. Much structural, mutagenesis, and kinetic data on FAAH has been generated over the last couple of decades. This has prompted several informative computational investigations to elucidate, at the atomic-level, mechanistic details on catalysis and inhibition of this pharmaceutically relevant enzyme. Here, we review how these computational studies - based on classical molecular dynamics, full quantum mechanics, and hybrid QM/MM methods - have clarified the binding and reactivity of some relevant substrates and inhibitors of FAAH. We also discuss the experimental implications of these computational insights, which have provided a thoughtful elucidation of the complex physical and chemical steps of the enzymatic mechanism of FAAH. Finally, we discuss how computations have been helpful for building structure-activity relationships of potent FAAH inhibitors.
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Affiliation(s)
- Giulia Palermo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy; Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy; Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Marco De Vivo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
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Bayse CA, Merz KM. Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations. Biochemistry 2014; 53:5034-41. [PMID: 25020142 DOI: 10.1021/bi500531p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23518, United States
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11
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Ochocki JD, Distefano MD. Prenyltransferase Inhibitors: Treating Human Ailments from Cancer to Parasitic Infections. MEDCHEMCOMM 2013; 4:476-492. [PMID: 25530833 DOI: 10.1039/c2md20299a] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The posttranslational modification of protein prenylation is a covalent lipid modification on the C-terminus of substrate proteins that serves to enhance membrane affinity. Oncogenic proteins such as Ras have this modification and significant effort has been placed into developing inhibitors of the prenyltransferase enzymes for clinical therapy. In addition to cancer therapy, prenyltransferase inhibitors have begun to find important therapeutic uses in other diseases, including progeria, hepatitis C and D, parasitic infections, and other maladies. This review will trace the evolution of prenyltransferase inhibitors from their initial use as cancer therapeutics to their expanded applications for other diseases.
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Affiliation(s)
- Joshua D Ochocki
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 (USA)
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12
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Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif. J Mol Model 2012; 19:673-88. [DOI: 10.1007/s00894-012-1590-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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13
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Yang Y, Miao Y, Wang B, Cui G, Merz KM. Catalytic mechanism of aromatic prenylation by NphB. Biochemistry 2012; 51:2606-18. [PMID: 22385275 DOI: 10.1021/bi201800m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NphB is an aromatic prenyltransferase that catalyzes the attachment of a 10-carbon geranyl group to aromatic substrates. Importantly, NphB exhibits a rich substrate selectivity and product regioselectivity. A systematic computational study has been conducted in order to address several question associated with NphB-catalyzed geranylation. The reaction mechanism of the prenylation step has been characterized as a S(N)1 type dissociative mechanism with a weakly stable carbocation intermediate. A novel π-chamber composed of Tyr121, Tyr216, and 1,6-DHN is found to be important in stabilizing the carbocation. The observed difference in the rates of product formation from 5- and 2-prenylation arises from the differing orientations of the aromatic substrate in the resting state. 4-Prenylation shares the same resting state with 5-prenylation, but the lower free energy barrier for carbocation formation makes the latter reaction more facile. The high free energy barrier associated with 7-prenylation is caused by the unfavorable orientation of 1,6-DHN in active site pocket, along with the difficulty of proton elimination after the prenylation step. A water-mediated proton transfer facilitates the loss of hydrogen at the prenylation site to form the final prenylated product. Interestingly, the same crystallographically observed water molecule has been found to be responsible for proton loss in all three experimentally identified products. After proton transfer, the relaxation of the final product from a sp(3) carbon center to a sp(2) center triggers a "spring-loaded" product release mechanism which pushes the final product out of the binding pocket toward the edge of the active site. The hydrogen bond interactions between the two hydroxyl groups of the aromatic product and the side chains of Ser214 and Tyr288 help to "steer" the movement of the product. In addition, mutagenesis studies identify these same two side chains as being responsible for the observed regioselectivity, particularly 2-prenylation. These observations provide valuable insights into NphB chemistry, offering an opportunity to better engineer the active site and to control the reactivity in order to obtain high yields of the desired product(s). Furthermore, the S(N)1 reaction mechanism observed for NphB differs from the prenylation reaction found in, for example, the farnesyltransferase, which proceeds via an S(N)2-like reaction pathway. The spring-loaded release mechanism highlighted herein also offers novel insights into how enzymes facilitate product release.
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Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States
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Yang Y, Wang B, Ucisik MN, Cui G, Fierke CA, Merz KM. Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. J Am Chem Soc 2012; 134:820-3. [PMID: 22206225 DOI: 10.1021/ja209650h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein farnesyltransferase (FTase) catalyzes farnesylation of a variety of peptide substrates. (3)H α-secondary kinetic isotope effect (α-SKIE) measurements of two peptide substrates, CVIM and CVLS, are significantly different and have been proposed to reflect a rate-limiting S(N)2-like transition state with dissociative characteristics for CVIM, while, due to the absence of an isotope effect, CVLS was proposed to have a rate-limiting peptide conformational change. Potential of mean force quantum mechanical/molecular mechanical studies coupled with umbrella sampling techniques were performed to further probe this mechanistic dichotomy. We observe the experimentally proposed transition state (TS) for CVIM but find that CVLS has a symmetric S(N)2 TS, which is also consistent with the absence of a (3)H α-SKIE. These calculations demonstrate facile substrate-dependent alterations in the transition state structure catalyzed by FTase.
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Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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Sousa SF, Fernandes PA, Ramos MJ. Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers. Phys Chem Chem Phys 2012; 14:12431-41. [DOI: 10.1039/c2cp41180f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Perez MAS, Sousa SF, Oliveira EFT, Fernandes PA, Ramos MJ. Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis. J Phys Chem B 2011; 115:15339-54. [DOI: 10.1021/jp205481y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marta A. S. Perez
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Eduardo F. T. Oliveira
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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Yang Y, Chakravorty DK, Merz KM. Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry 2011; 49:9658-66. [PMID: 20923173 DOI: 10.1021/bi1008358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies aimed at elucidating the unknown Mg2+ binding site in protein farnesyltransferase (FTase) are reported. FTase catalyzes the transfer of a farnesyl group to a conserved cysteine residue (Cys1p) on a target protein, an important step for proteins in the signal transduction pathways (e.g., Ras). Mg2+ ions accelerate the protein farnesylation reaction by up to 700-fold. The exact function of Mg2+ in catalysis and the structural characteristics of its binding remain unresolved to date. Molecular dynamics (MD) simulations addressing the role of magnesium ions in FTase are presented, and relevant octahedral binding motifs for Mg2+ in wild-type (WT) FTase and the Dβ352A mutant are explored. Our simulations suggest that the addition of Mg2+ ions causes a conformational change to occur in the FTase active site, breaking interactions known to keep FPP in its inactive conformation. Two relevant Mg2+ ion binding motifs were determined in WT FTase. In the first binding motif, WT1, the Mg2+ ion is coordinated to D352β, zinc-bound D297β, two water molecules, and one oxygen atom from the α- and β-phosphates of farnesyl diphosphate (FPP). The second binding motif, WT2, is identical with the exception of the zinc-bound D297β being replaced by a water molecule in the Mg2+ coordination complex. In the Dβ352A mutant Mg2+ binding motif, D297β, three water molecules, and one oxygen atom from the α- and β-phosphates of FPP complete the octahedral coordination sphere of Mg2+. Simulations of WT FTase, in which Mg2+ was replaced by water in the active site, recreated the salt bridges and hydrogen-bonding patterns around FPP, validating these simulations. In all Mg2+ binding motifs, a key hydrogen bond was identified between a magnesium-bound water and Cys1p, bridging the two metallic binding sites and, thereby, reducing the equilibrium distance between the reacting atoms of FPP Cys1p. The free energy profiles calculated for these systems provide a qualitative understanding of experimental results. They demonstrate that the two reactive atoms approach each other more readily in the presence of Mg2+ in WT FTase and mutant. The flexible WT2 model was found to possess the lowest barrier toward the conformational change, suggesting it is the preferred Mg2+ binding motif in WT FTase. In the mutant, the absence of D352β makes the transition toward a conformational change harder. Our calculations find support for the proposal that D352β performs a critical role in Mg2+ binding and Mg2+ plays an important role in the conformational transition step.
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Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, University of Florida, Gainesville, FL 32611-8435, USA
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18
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Tantillo DJ. Biosynthesis via carbocations: theoretical studies on terpene formation. Nat Prod Rep 2011; 28:1035-53. [PMID: 21541432 DOI: 10.1039/c1np00006c] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review describes applications of quantum chemical calculations in the field of terpene biosynthesis, with a focus on insights into the mechanisms of terpene-forming carbocation rearrangements arising from theoretical studies.
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19
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Aue DH. Carbocations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hari Narayana Moorthy NS, Sousa SF, Ramos MJ, Fernandes PA. Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors. J Enzyme Inhib Med Chem 2011; 26:777-91. [DOI: 10.3109/14756366.2011.552885] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- N. S. Hari Narayana Moorthy
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Sergio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
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Nguyen UTT, Goody RS, Alexandrov K. Understanding and exploiting protein prenyltransferases. Chembiochem 2010; 11:1194-201. [PMID: 20432425 DOI: 10.1002/cbic.200900727] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Uyen T T Nguyen
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA
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22
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Sit PHL, Migliore A, Ho MH, Klein ML. Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron−Dioxygen Intermediates and Proton Transfer in Superoxide Reductase. J Chem Theory Comput 2010; 6:2896-909. [DOI: 10.1021/ct900599q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick H.-L. Sit
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
| | - Agostino Migliore
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
| | - Ming-Hsun Ho
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
| | - Michael L. Klein
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-3034-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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