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Grear T, Avery C, Patterson J, Jacobs DJ. Molecular function recognition by supervised projection pursuit machine learning. Sci Rep 2021; 11:4247. [PMID: 33608593 PMCID: PMC7895977 DOI: 10.1038/s41598-021-83269-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
Identifying mechanisms that control molecular function is a significant challenge in pharmaceutical science and molecular engineering. Here, we present a novel projection pursuit recurrent neural network to identify functional mechanisms in the context of iterative supervised machine learning for discovery-based design optimization. Molecular function recognition is achieved by pairing experiments that categorize systems with digital twin molecular dynamics simulations to generate working hypotheses. Feature extraction decomposes emergent properties of a system into a complete set of basis vectors. Feature selection requires signal-to-noise, statistical significance, and clustering quality to concurrently surpass acceptance levels. Formulated as a multivariate description of differences and similarities between systems, the data-driven working hypothesis is refined by analyzing new systems prioritized by a discovery-likelihood. Utility and generality are demonstrated on several benchmarks, including the elucidation of antibiotic resistance in TEM-52 beta-lactamase. The software is freely available, enabling turnkey analysis of massive data streams found in computational biology and material science.
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Affiliation(s)
- Tyler Grear
- grid.266859.60000 0000 8598 2218Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28262 USA
| | - Chris Avery
- grid.266859.60000 0000 8598 2218Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28262 USA ,grid.266859.60000 0000 8598 2218Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28262 USA
| | - John Patterson
- grid.266859.60000 0000 8598 2218Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28262 USA
| | - Donald J. Jacobs
- grid.266859.60000 0000 8598 2218Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28262 USA ,grid.266859.60000 0000 8598 2218Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28262 USA
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ElSawy KM, Verma CS, Joseph TL, Lane DP, Twarock R, Caves LSD. On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study. Cell Cycle 2013; 12:394-404. [PMID: 23324352 DOI: 10.4161/cc.23511] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The interaction of p53 with its regulators MDM2 and MDMX plays a major role in regulating the cell cycle. Inhibition of this interaction has become an important therapeutic strategy in oncology. Although MDM2 and MDMX share a very high degree of sequence/structural similarity, the small-molecule inhibitor nutlin appears to be an efficient inhibitor only of the p53-MDM2 interaction. Here, we investigate the mechanism of interaction of nutlin with these two proteins and contrast it with that of p53 using Brownian dynamics simulations. In contrast to earlier attempts to examine the bound states of the partners, here we locate initial reaction events in these interactions by identifying the regions of space around MDM2/MDMX, where p53/nutlin experience associative encounters with prolonged residence times relative to that in bulk solution. We find that the initial interaction of p53 with MDM2 is long-lived relative to nutlin, but, unlike nutlin, it takes place at the N- and C termini of the MDM2 protein, away from the binding site, suggestive of an allosteric mechanism of action. In contrast, nutlin initially interacts with MDM2 directly at the clefts of the binding site. The interaction of nutlin with MDMX, however, is very short-lived compared with MDM2 and does not show such direct initial interactions with the binding site. Comparison of the topology of the electrostatic potentials of MDM2 and MDMX and the locations of the initial encounters with p53/nutlin in tandem with structure-based sequence alignment revealed that the origin of the diminished activity of nutlin toward MDMX relative to MDM2 may stem partly from the differing topologies of the electrostatic potentials of the two proteins. Glu25 and Lys51 residues underpin these topological differences and appear to collectively play a key role in channelling nutlin directly toward the binding site on the MDM2 surface and are absent in MDMX. The results, therefore, provide new insight into the mechanism of p53/nutlin interactions with MDM2 and MDMX and could potentially have a broader impact on anticancer drug optimization strategies.
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Affiliation(s)
- Karim M ElSawy
- York Centre for Complex Systems Analysis (YCCSA), University of York, York, UK.
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Fuller JC, Jackson RM, Edwards TA, Wilson AJ, Shirts MR. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable. PLoS One 2012; 7:e43253. [PMID: 22916232 PMCID: PMC3423354 DOI: 10.1371/journal.pone.0043253] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/18/2012] [Indexed: 12/04/2022] Open
Abstract
The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.
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Affiliation(s)
- Jonathan C. Fuller
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Richard M. Jackson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Andrew J. Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Michael R. Shirts
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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Lu SY, Jiang YJ, Zou JW, Wu TX. Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based α-helix mimetic as dual inhibitors of MDM2 and MDMX. J Mol Graph Model 2011; 30:167-78. [PMID: 21820342 DOI: 10.1016/j.jmgm.2011.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 01/09/2023]
Abstract
Inhibition of the interactions between the tumor suppressor protein p53 and its negative regulators, the MDM2 and MDMX oncogenic proteins, is increasingly gaining interest in cancer therapy and drug design. In this study, we carry out molecular docking, molecular dynamics (MD) simulations, and molecular mechanics Poisson-Boltzmann and generalized Born/surface area (MM-PB/GBSA) binding free energy calculations on an active compound 3a and an inactive compound NC-1, which share a common pyrrolopyrimidine-based scaffold. MD simulations and MM-PB/GBSA calculations show that the compound NC-1 may not bind to MDM2 and MDMX, in agreement with the experimental results. Detailed MM-PB/GBSA calculations on the MDM2-3a and MDMX-3a complexes unravel that the binding free energies are similar for the two complexes. Furthermore, the van der Waals energy is the largest component of the binding free energy for both complexes, which indicates that the interactions between the compound 3a and MDM2 and MDMX are dominated by shape complementarity. In addition, the analysis of individual residue contribution and protein-ligand binding mode show that the three functional groups on R₁, R₂, and R₃ of the compound 3a can mimic the spatial orientation of the side chains of Phe19, Trp23, and Leu26 of p53, respectively. The obtained computational results suggest that the compound 3a can act as a dual inhibitor of MDM2-p53 and MDMX-p53 interactions, consistent with the experimental results.
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Affiliation(s)
- Shao-Yong Lu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, PR China
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Dezi C, Carotti A, Magnani M, Baroni M, Padova A, Cruciani G, Macchiarulo A, Pellicciari R. Molecular Interaction Fields and 3D-QSAR Studies of p53−MDM2 Inhibitors Suggest Additional Features of Ligand−Target Interaction. J Chem Inf Model 2010; 50:1451-65. [DOI: 10.1021/ci100113p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cristina Dezi
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Andrea Carotti
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Matteo Magnani
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Massimo Baroni
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Alessandro Padova
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Gabriele Cruciani
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Antonio Macchiarulo
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
| | - Roberto Pellicciari
- Dipartimento di Chimica e Tecnologia del Farmaco, Università di Perugia, via del Liceo 1, 06123 Perugia, Italy, Siena Biotech S.p.A., Strada del Petriccio e Belriguardo, 35, 53100, Siena, Italy, Molecular Discovery Ltd, 215 Marsh Road, Pinner, Middlesex HA55NE, England, and Laboratory for Chemometrics and Cheminformatics, Department of Chemistry, Università di Perugia, via Elce di Sotto 10, 06123 Perugia, Italy
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