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Šponer JE, Šponer J, Výravský J, Matyášek R, Kovařík A, Dudziak W, Ślepokura K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. iScience 2023; 26:107600. [PMID: 37664611 PMCID: PMC10470394 DOI: 10.1016/j.isci.2023.107600] [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: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o, Libušina třída 1, 62300 Brno, Czech Republic
- Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Wojciech Dudziak
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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2
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Ray D, Parrinello M. Kinetics from Metadynamics: Principles, Applications, and Outlook. J Chem Theory Comput 2023; 19:5649-5670. [PMID: 37585703 DOI: 10.1021/acs.jctc.3c00660] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Metadynamics is a popular enhanced sampling algorithm for computing the free energy landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary and Parrinello introduced the infrequent metadynamics approach for calculating the kinetics of transitions across free energy barriers. Since then, metadynamics-based methods for obtaining rate constants have attracted significant attention in computational molecular science. Such methods have been applied to study a wide range of problems, including protein-ligand binding, protein folding, conformational transitions, chemical reactions, catalysis, and nucleation. Here, we review the principles of elucidating kinetics from metadynamics-like approaches, subsequent methodological developments in this area, and successful applications on chemical, biological, and material systems. We also highlight the challenges of reconstructing accurate kinetics from enhanced sampling simulations and the scope of future developments.
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Affiliation(s)
- Dhiman Ray
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
| | - Michele Parrinello
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
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3
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Zlobin A, Golovin A. Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme-Substrate Complex. ACS OMEGA 2022; 7:40279-40292. [PMID: 36385818 PMCID: PMC9647873 DOI: 10.1021/acsomega.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The cysteine protease from the tobacco etch virus (TEVp) is a well-known and widely utilized enzyme. TEVp's chymotrypsin-like fold is generally associated with serine catalytic triads that differ in terms of a reaction mechanism from the most well-studied papain-like cysteine proteases. The question of what dominates the TEVp mechanism, nucleophile identity, or structural composition has never been previously addressed. Here, we use enhanced sampling multiscale modeling to uncover that TEVp combines the features of two worlds in such a way that potentially hampers its activity. We show that TEVp cysteine is strictly in the anionic form in a free enzyme similar to papain. Peptide binding shifts the equilibrium toward the nucleophile's protonated form, characteristic of chymotrypsin-like proteases, although the cysteinyl anion form is still present and interconversion is rapid. This way cysteine protonation generates enzyme states that are a diversion from the most effective course of action, with only 13.2% of Michaelis complex sub-states able to initiate the reaction. As a result, we propose an updated view on the reaction mechanism catalyzed by TEVp. We also demonstrate that AlphaFold is able to construct protease-substrate complexes with high accuracy. We propose that our findings open a way for its industrious use in enzymological tasks. Unique features of TEVp discovered in this work open a discussion on the evolutionary history and trade-offs of optimizing serine triad-associated folds to cysteine as a nucleophile.
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Affiliation(s)
- Alexander Zlobin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrey Golovin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius
University of Science and Technology, 354340 Sochi, Russia
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4
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Marinova V, Wood GPF, Marziano I, Salvalaglio M. Investigating the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets. CRYSTAL GROWTH & DESIGN 2022; 22:3034-3041. [PMID: 35529061 PMCID: PMC9073942 DOI: 10.1021/acs.cgd.1c01479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Surface defects play a crucial role in the process of crystal growth, as incorporation of growth units generally takes place on undercoordinated sites on the growing crystal facet. In this work, we use molecular simulations to obtain information on the role of the solvent in the roughening of three morphologically relevant crystal faces of form I of racemic ibuprofen. To this aim, we devise a computational strategy to evaluate the energetic cost associated with the formation of a surface vacancy for a set of ten solvents, covering a range of polarities and hydrogen bonding propensities. We find that the mechanism as well as the work of defect formation are markedly solvent and facet dependent. Based on Mean Force Integration and Well Tempered Metadynamics, the methodology developed in this work has been designed with the aim of capturing solvent effects at the atomistic scale while maintaining the computational efficiency necessary for implementation in high-throughput in-silico screenings of crystallization solvents.
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Affiliation(s)
- Veselina Marinova
- Department
of Materials Science and Engineering, The
University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Geoffrey P. F. Wood
- Pfizer
Worldwide Research and Development, Groton Laboratories, Groton, Connecticut 06340, United States
| | - Ivan Marziano
- Pfizer
Worldwide Research and Development, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Matteo Salvalaglio
- Thomas
Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
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5
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Vasilopoulos Y, Heyda J, Rohlíček J, Skořepová E, Zvoníček V, Šoóš M. Impact of Solvent-Drug Interactions on the Desolvation of a Pharmaceutical Solvate. J Phys Chem B 2022; 126:503-512. [PMID: 34994565 DOI: 10.1021/acs.jpcb.1c07655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In drug manufacturing, solvent-based methods are used for the crystallization of active pharmaceutical ingredients (APIs). Often, the solvent interacts with the API resulting in the formation of a new solid compound, the solvate. When desolvation occurs upon heating, it might result in the formation of new solid forms with significantly different physicochemical properties. Therefore, in this work, we study the desolvation kinetics by combining in situ powder X-ray diffraction (PXRD), all-atom molecular dynamics (MD) simulations, and macroscopic solid-state reaction kinetics modeling. The fluorobenzene (FB) solvate of Bruton's tyrosine kinase inhibitor Ibrutinib (IBR) was used as a model system. While the macroscopic solid-state modeling provides information about the desolvation kinetics, the MD simulations were used to trace individual FB molecules inside the crystal lattice. The activation energy of confined solvent diffusion, obtained by MD simulations, agrees well with results of the macroscopic solid-state reaction kinetics modeling. In addition, MD simulations provided detailed information about the IBR-FB interactions at the nanoscale. The mechanism revealed is that the solvent molecules diffusion, controlled by distinct open-close gating conformational changes of the drug, triggers the desolvation throughout the crystal lattice.
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Affiliation(s)
- Yannis Vasilopoulos
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 3, 16628 Prague 6, Czech Republic
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 3, 16628 Prague 6, Czech Republic
| | - Jan Rohlíček
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Eliška Skořepová
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 3, 16628 Prague 6, Czech Republic.,Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Vítek Zvoníček
- Zentiva, k.s., U kabelovny 130, 10237 Prague 10, Czech Republic
| | - Miroslav Šoóš
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 3, 16628 Prague 6, Czech Republic
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Marinova V, Dodd L, Lee SJ, Wood GPF, Marziano I, Salvalaglio M. Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering. J Chem Inf Model 2021; 61:2263-2273. [PMID: 33913713 PMCID: PMC8278389 DOI: 10.1021/acs.jcim.0c01387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a systematic approach for the identification of statistically relevant conformational macrostates of organic molecules from molecular dynamics trajectories. The approach applies to molecules characterized by an arbitrary number of torsional degrees of freedom and enables the transferability of the macrostates definition across different environments. We formulate a dissimilarity measure between molecular configurations that incorporates information on the characteristic energetic cost associated with transitions along all relevant torsional degrees of freedom. Such metric is employed to perform unsupervised clustering of molecular configurations based on the Fast Search and Find of Density Peaks algorithm. We apply this method to investigate the equilibrium conformational ensemble of Sildenafil, a conformationally complex pharmaceutical compound, in different environments including the crystal bulk, the gas phase, and three different solvents (acetonitrile, 1-butanol, and toluene). We demonstrate that while Sildenafil can adopt more than 100 metastable conformational configurations, only 12 are significantly populated across all of the environments investigated. Despite the complexity of the conformational space, we find that the most abundant conformers in solution are the closest to the conformers found in the most common Sildenafil crystal phase.
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Affiliation(s)
- Veselina Marinova
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K.,Department of Materials Science and Engineering, The University of Sheffield, Sheffield S1 3JD, U.K
| | - Laurence Dodd
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K
| | - Song-Jun Lee
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K
| | - Geoffrey P F Wood
- Pfizer Worldwide Research and Development, Groton Laboratories, Groton, Connecticut 06340, United States
| | - Ivan Marziano
- Pfizer Worldwide Research and Development, Sandwich CT13 9NJ, Kent, U.K
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K
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Francia NF, Price LS, Salvalaglio M. Reducing crystal structure overprediction of ibuprofen with large scale molecular dynamics simulations. CrystEngComm 2021. [DOI: 10.1039/d1ce00616a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reduction of a large dataset of computationally predicted structures of ibuprofen by employing molecular dynamics and biased simulations at finite temperature and pressure.
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Affiliation(s)
- Nicholas F. Francia
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, UK
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, UK
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Tang SK, Davey RJ, Sacchi P, Cruz-Cabeza AJ. Can molecular flexibility control crystallization? The case of para substituted benzoic acids. Chem Sci 2020; 12:993-1000. [PMID: 34163865 PMCID: PMC8179050 DOI: 10.1039/d0sc05424k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Despite the technological importance of crystallization from solutions almost nothing is known about the relationship between the kinetic process of nucleation and the molecular and crystal structures of a crystallizing solute. Nowhere is this more apparent than in our attempts to understand the behavior of increasingly large, flexible molecules developed as active components in the pharmaceutical arena. In our current contribution we develop a general protocol involving a combination of computation (conformation analysis, lattice energy), and experiment (measurement of nucleation rates), and show how significant advances can be made. We present the first systematic study aimed at quantifying the impact of molecular flexibility on nucleation kinetics. The nucleation rates of 4 para substituted benzoic acids are compared, two of which have substituents with flexible chains. In making this comparison, the importance of normalizing data to account for differing solubilities is highlighted. These data have allowed us to go beyond popular qualitative descriptors such ‘crystallizability’ or ‘crystallization propensity’ in favour of more precise nucleation rate data. Overall, this leads to definite conclusions as to the relative importance of solution chemistry, solid-state interactions and conformational flexibility in the crystallization of these molecules and confirms the key role of intermolecular stacking interactions in determining relative nucleation rates. In a more general sense, conclusions are drawn as to conditions under which conformational change may become rate determining during a crystallization process. Little is known about the relationship between the kinetic process of nucleation and the molecular and crystal structures of a crystallizing solute. Here we compare the behaviour of a series of benzoic acids with a focus on conformational effects.![]()
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Affiliation(s)
- Sin Kim Tang
- Department of Chemical Engineering and Analytical Science, School of Engineering, University of Manchester M13PL UK
| | - Roger J Davey
- Department of Chemical Engineering and Analytical Science, School of Engineering, University of Manchester M13PL UK
| | - Pietro Sacchi
- Department of Chemical Engineering and Analytical Science, School of Engineering, University of Manchester M13PL UK
| | - Aurora J Cruz-Cabeza
- Department of Chemical Engineering and Analytical Science, School of Engineering, University of Manchester M13PL UK
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Marinova V, Salvalaglio M. Time-independent free energies from metadynamics via mean force integration. J Chem Phys 2019; 151:164115. [DOI: 10.1063/1.5123498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Veselina Marinova
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
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