1
|
Palma J, Pierdominici-Sottile G. Fortuitous Correlations in Molecular Dynamics Simulations: Their Harmful Influence on the Probability Distributions of the Main Principal Components. ACS OMEGA 2024; 9:20488-20501. [PMID: 38737025 PMCID: PMC11080035 DOI: 10.1021/acsomega.4c01515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
Nonsense correlations frequently develop between independent random variables that evolve with time. Therefore, it is not surprising that they appear between the components of vectors carrying out multidimensional random walks, such as those describing the trajectories of biomolecules in molecular dynamics simulations. The existence of these correlations does not imply in itself a problem. Still, it can present a problem when the trajectories are analyzed with an algorithm such as the Principal Component Analysis (PCA) because it seeks to maximize correlations without discriminating whether they have physical origin or not. In this Article, we employ random walks occurring on multidimensional harmonic potentials to evaluate the influence of fortuitous correlations in PCA. We demonstrate that, because of them, this algorithm affords misleading results when applied to a single trajectory. The errors do not only affect the directions of the first eigenvectors and their eigenvalues, but the very definition of the molecule's "essential space" may be wrong. Additionally, the main principal component's probability distributions present artificial structures which do not correspond with the shape of the potential energy surface. Finally, we show that the PCA of two realistic protein models, human serum albumin and lysozyme, behave similarly to the simple harmonic models. In all cases, the problems can be mitigated and eventually eliminated by doing PCA on concatenated trajectories formed from a large enough number of individual simulations.
Collapse
Affiliation(s)
- Juliana Palma
- Departamento
de Ciencia y Tecnología, Universidad
Nacional de Quilmes, Sáenz Peña 352 Bernal, Buenos
Aires B1876BXD, Argentina
- Consejo
Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento
de Ciencia y Tecnología, Universidad
Nacional de Quilmes, Sáenz Peña 352 Bernal, Buenos
Aires B1876BXD, Argentina
- Consejo
Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| |
Collapse
|
2
|
Palma J, Pierdominici-Sottile G. On the Uses of PCA to Characterise Molecular Dynamics Simulations of Biological Macromolecules: Basics and Tips for an Effective Use. Chemphyschem 2023; 24:e202200491. [PMID: 36285677 DOI: 10.1002/cphc.202200491] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/24/2022] [Indexed: 01/20/2023]
Abstract
Principal Component Analysis (PCA) is a procedure widely used to examine data collected from molecular dynamics simulations of biological macromolecules. It allows for greatly reducing the dimensionality of their configurational space, facilitating further qualitative and quantitative analysis. Its simplicity and relatively low computational cost explain its extended use. However, a judicious implementation of PCA requires the knowledge of its theoretical grounds as well as its weaknesses and capabilities. In this article, we review these issues and discuss several strategies developed over the last years to mitigate the main PCA flaws and enhance the reproducibility of its results.
Collapse
Affiliation(s)
- Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes.,Consejo Nacional de Investigaciones Científicas y Técnicas
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes.,Consejo Nacional de Investigaciones Científicas y Técnicas
| |
Collapse
|
3
|
Bolivar-Muñoz J, Vits S, Bermudez-Santana CI, Galindo JF. Structural Analysis of the Spike Protein of SARS-CoV-2 Variants and Other Betacoronaviruses Using Molecular Dynamics. Chemphyschem 2022; 23:e202200382. [PMID: 35927218 DOI: 10.1002/cphc.202200382] [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: 06/06/2022] [Revised: 08/03/2022] [Indexed: 01/04/2023]
Abstract
A structural analysis over various spike proteins from three highly pathogenic Betacoronavirus was done to understand their structural differences. The proteins were modeled using crystal structures from SARS-CoV, MERS-CoV, and other Betacoronavirus that infect bats and pangolins. The group was split in two sets; the first set corresponds to the non-mutated spike proteins, while the second set corresponds to mutated spike variants alpha, beta, gamma, delta, omicron and mu; five of them classified as variants of concern and the last one as variant of interest. A conformational space exploration was carried out for every protein by using molecular dynamic simulations. Root mean square fluctuations, principal component and cross-correlation analysis were carried out over the dynamics to analyze the flexibility and rigidity of every protein in comparison to the wild type Spike protein from the SARS-CoV-2. The obtained results indicate that the proteins, which are not spread among humans, have smooth movements compared to those of SARS-CoV-2 and its variants. In addition, a relationship between the speed of the virulence and the movement of the protein can explain the behavior of delta and omicron variants.
Collapse
Affiliation(s)
- Jonathan Bolivar-Muñoz
- Department of Chemistry, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Sofia Vits
- Department of Biology, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Clara Isabel Bermudez-Santana
- Department of Biology, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Johan Fabian Galindo
- Department of Chemistry, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| |
Collapse
|
4
|
Pharmacophore model-aided virtual screening combined with comparative molecular docking and molecular dynamics for identification of marine natural products as SARS-CoV-2 papain-like protease inhibitors. ARAB J CHEM 2022; 15:104334. [PMID: 36246784 PMCID: PMC9554199 DOI: 10.1016/j.arabjc.2022.104334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Targeting SARS-CoV-2 papain-like protease using inhibitors is a suitable approach for inhibition of virus replication and dysregulation of host anti-viral immunity. Engaging all five binding sites far from the catalytic site of PLpro is essential for developing a potent inhibitor. We developed and validated a structure-based pharmacophore model with 9 features of a potent PLpro inhibitor. The pharmacophore model-aided virtual screening of the comprehensive marine natural product database predicted 66 initial hits. This hit library was downsized by filtration through a molecular weight filter of ≤ 500 g/mol. The 50 resultant hits were screened by comparative molecular docking using AutoDock and AutoDock Vina. Comparative molecular docking enables benchmarking docking and relieves the disparities in the search and scoring functions of docking engines. Both docking engines retrieved 3 same compounds at different positions in the top 1 % rank, hence consensus scoring was applied, through which CMNPD28766, aspergillipeptide F emerged as the best PLpro inhibitor. Aspergillipeptide F topped the 50-hit library with a pharmacophore-fit score of 75.916. Favorable binding interactions were predicted between aspergillipeptide F and PLpro similar to the native ligand XR8-24. Aspergillipeptide F was able to engage all the 5 binding sites including the newly discovered BL2 groove, site V. Molecular dynamics for quantification of Cα-atom movements of PLpro after ligand binding indicated that it exhibits highly correlated domain movements contributing to the low free energy of binding and a stable conformation. Thus, aspergillipeptide F is a promising candidate for pharmaceutical and clinical development as a potent SARS-CoV-2 PLpro inhibitor.
Collapse
Key Words
- CMNPD, comprehensive marine natural product database
- Consensus scoring
- DCCM, dynamic cross-correlation matrix
- H, hydrophobic
- HBA, hydrogen bond acceptor
- HBD, hydrogen bond donor
- MD, molecular dynamics
- MMGBSA, molecular mechanics generalized Born and surface area continuum solvation
- MW, molecular weight
- Marine natural products
- Molecular docking
- Molecular dynamics
- PCA, principal component analysis
- PI, positive ionization
- PLpro, SARS-CoV-2 papain-like protease
- Pharmacophore model
- SARS-CoV-2 PLpro
- TG, Total gain
- ns, nanoseconds
- ps, picoseconds
Collapse
|
5
|
Andújar SA, Gutiérrez LJ, Enriz RD, Baldoni HA. Structure, interface stability and hot-spots identification for RBD(SARS-CoV-2):hACE2 complex formation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1979229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sebastián A. Andújar
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Lucas J. Gutiérrez
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Ricardo D. Enriz
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, Institute of Applied Mathematics of San Luis (IMASL. CONICET), National University of San Luis, San Luis, Argentina
| |
Collapse
|
6
|
Ormazábal A, Palma J, Pierdominici-Sottile G. Molecular Dynamics Simulations Unveil the Basis of the Sequential Binding of RsmE to the Noncoding RNA RsmZ. J Phys Chem B 2021; 125:3045-3056. [PMID: 33755488 DOI: 10.1021/acs.jpcb.0c09770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CsrA/RsmE are dimeric proteins that bind to targeted mRNAs repressing translation. This mechanism modulates several metabolic pathways and allows bacteria to efficiently adjust their responses to environmental changes. In turn, small RNAs (sRNA) such as CsrB or RsmZ, restore translation by sequestering CsrA/RsmE dimers. Thus, these molecules act in tandem as a gene-expression regulatory system. Recently, a combined NMR-EPR approach solved the structure of part of RsmZ of Pseudomonas fluorescens, attached to three RsmE dimers. The study demonstrated that RsmE assembles onto RsmZ following a specific sequential order. The reasons underlying this peculiar behavior are still unclear. Here, we present a molecular dynamics analysis that explores the conformational diversity of RsmZ and RsmZ-RsmE complexes. The results reveal a clear pattern regarding the exposure of the alternative GGA binding motifs of RsmZ. This pattern is tuned by the attachment of RsmE dimers. Altogether, the observations provide a simple and convincing explanation for the order observed in the sequestration of RsmE dimers. Typical structures for RsmZ and RsmZ-RsmE complexes have been identified. Their characteristics concerning the exposure of the GGA sequences are presented and their most significant interactions are described.
Collapse
Affiliation(s)
- Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | | |
Collapse
|
7
|
Windsor PK, Plassmeyer SP, Mattock DS, Bradfield JC, Choi EY, Miller BR, Han BH. Biflavonoid-Induced Disruption of Hydrogen Bonds Leads to Amyloid-β Disaggregation. Int J Mol Sci 2021; 22:ijms22062888. [PMID: 33809196 PMCID: PMC8001082 DOI: 10.3390/ijms22062888] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/03/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Deposition of amyloid β (Aβ) fibrils in the brain is a key pathologic hallmark of Alzheimer’s disease. A class of polyphenolic biflavonoids is known to have anti-amyloidogenic effects by inhibiting aggregation of Aβ and promoting disaggregation of Aβ fibrils. In the present study, we further sought to investigate the structural basis of the Aβ disaggregating activity of biflavonoids and their interactions at the atomic level. A thioflavin T (ThT) fluorescence assay revealed that amentoflavone-type biflavonoids promote disaggregation of Aβ fibrils with varying potency due to specific structural differences. The computational analysis herein provides the first atomistic details for the mechanism of Aβ disaggregation by biflavonoids. Molecular docking analysis showed that biflavonoids preferentially bind to the aromatic-rich, partially ordered N-termini of Aβ fibril via the π–π interactions. Moreover, docking scores correlate well with the ThT EC50 values. Molecular dynamic simulations revealed that biflavonoids decrease the content of β-sheet in Aβ fibril in a structure-dependent manner. Hydrogen bond analysis further supported that the substitution of hydroxyl groups capable of hydrogen bond formation at two positions on the biflavonoid scaffold leads to significantly disaggregation of Aβ fibrils. Taken together, our data indicate that biflavonoids promote disaggregation of Aβ fibrils due to their ability to disrupt the fibril structure, suggesting biflavonoids as a lead class of compounds to develop a therapeutic agent for Alzheimer’s disease.
Collapse
Affiliation(s)
- Peter K. Windsor
- Department of Chemistry, Truman State University, Kirksville, MO 63501, USA; (P.K.W.); (S.P.P.); (D.S.M.); (J.C.B.)
| | - Stephen P. Plassmeyer
- Department of Chemistry, Truman State University, Kirksville, MO 63501, USA; (P.K.W.); (S.P.P.); (D.S.M.); (J.C.B.)
| | - Dominic S. Mattock
- Department of Chemistry, Truman State University, Kirksville, MO 63501, USA; (P.K.W.); (S.P.P.); (D.S.M.); (J.C.B.)
| | - Jonathan C. Bradfield
- Department of Chemistry, Truman State University, Kirksville, MO 63501, USA; (P.K.W.); (S.P.P.); (D.S.M.); (J.C.B.)
| | - Erika Y. Choi
- Department of Pharmacology, A.T. Still University, Kirksville, MO 63501, USA;
| | - Bill R. Miller
- Department of Chemistry, Truman State University, Kirksville, MO 63501, USA; (P.K.W.); (S.P.P.); (D.S.M.); (J.C.B.)
- Correspondence: (B.R.M.III); (B.H.H.)
| | - Byung Hee Han
- Department of Pharmacology, A.T. Still University, Kirksville, MO 63501, USA;
- Correspondence: (B.R.M.III); (B.H.H.)
| |
Collapse
|
8
|
Saltalamacchia A, Casalino L, Borišek J, Batista VS, Rivalta I, Magistrato A. Decrypting the Information Exchange Pathways across the Spliceosome Machinery. J Am Chem Soc 2020; 142:8403-8411. [PMID: 32275149 PMCID: PMC7339022 DOI: 10.1021/jacs.0c02036] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intron splicing of a nascent mRNA transcript by spliceosome (SPL) is a hallmark of gene regulation in eukaryotes. SPL is a majestic molecular machine composed of an entangled network of proteins and RNAs that meticulously promotes intron splicing through the formation of eight intermediate complexes. Cross-communication among the critical distal proteins of the SPL assembly is pivotal for fast and accurate directing of the compositional and conformational readjustments necessary to achieve high splicing fidelity. Here, molecular dynamics (MD) simulations of an 800 000 atom model of SPL C complex from yeast Saccharomyces cerevisiae and community network analysis enabled us to decrypt the complexity of this huge molecular machine, by identifying the key channels of information transfer across long distances separating key protein components. The reported study represents an unprecedented attempt in dissecting cross-communication pathways within one of the most complex machines of eukaryotic cells, supporting the critical role of Clf1 and Cwc2 splicing cofactors and specific domains of the Prp8 protein as signal conveyors for pre-mRNA maturation. Our findings provide fundamental advances into mechanistic aspects of SPL, providing a conceptual basis for controlling the SPL via small-molecule modulators able to tackle splicing-associated diseases by altering/obstructing information-exchange paths.
Collapse
Affiliation(s)
- Andrea Saltalamacchia
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento 4, 40126 Bologna, Italy
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1 Laboratoire de Chimie, F69342, Lyon, France
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali, International School for Advanced Studies (SISSA), via Bonomea 265, 34135 Trieste, Italy
| |
Collapse
|
9
|
Protein targets of thiazolidinone derivatives in Toxoplasma gondii and insights into their binding to ROP18. BMC Genomics 2018; 19:856. [PMID: 30497375 PMCID: PMC6267824 DOI: 10.1186/s12864-018-5223-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 11/05/2018] [Indexed: 01/20/2023] Open
Abstract
Background Thiazolidinone derivatives show inhibitory activity (IC50) against the Toxoplasma gondii parasite, as well as high selectivity with high therapeutic index. To disclose the target proteins of the thiazolidinone core in this parasite, we explored in silico the active sites of different T. gondii proteins and estimated the binding-free energy of reported thiazolidinone molecules with inhibitory effect on invasion and replication of the parasite inside host cells. This enabled us to describe some of the most suitable structural characteristics to design a compound derived from the thiazolidinone core. Results The best binding affinity was observed in the active site of kinase proteins, we selected the active site of the T. gondii ROP18 kinase, because it is an important factor for the virulence and survival of the parasite. We present the possible effect of a derivative of thiazolidinone core in the active site of T. gondii ROP18 and described some characteristics of substituent groups that could improve the affinity and specificity of compounds derived from the thiazolidinone core against T. gondii. Conclusions The results of our study suggest that compounds derived from the thiazolidinone core have a preference for protein kinases of T. gondii, being promising compounds for the development of new drugs with potential anti-toxoplasmosis activity. Our findings highlight the importance of use computational studies for the understanding of the action mechanism of compounds with biological activity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5223-7) contains supplementary material, which is available to authorized users.
Collapse
|
10
|
Cossio-Pérez R, Palma J, Pierdominici-Sottile G. Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins. J Chem Inf Model 2017; 57:826-834. [PMID: 28301154 DOI: 10.1021/acs.jcim.6b00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
Collapse
Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| |
Collapse
|