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Perez JJ, Perez RA, Perez A. Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering. Front Mol Biosci 2021; 8:681617. [PMID: 34095231 PMCID: PMC8173110 DOI: 10.3389/fmolb.2021.681617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions (PPIs) mediate a large number of important regulatory pathways. Their modulation represents an important strategy for discovering novel therapeutic agents. However, the features of PPI binding surfaces make the use of structure-based drug discovery methods very challenging. Among the diverse approaches used in the literature to tackle the problem, linear peptides have demonstrated to be a suitable methodology to discover PPI disruptors. Unfortunately, the poor pharmacokinetic properties of linear peptides prevent their direct use as drugs. However, they can be used as models to design enzyme resistant analogs including, cyclic peptides, peptide surrogates or peptidomimetics. Small molecules have a narrower set of targets they can bind to, but the screening technology based on virtual docking is robust and well tested, adding to the computational tools used to disrupt PPI. We review computational approaches used to understand and modulate PPI and highlight applications in a few case studies involved in physiological processes such as cell growth, apoptosis and intercellular communication.
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Affiliation(s)
- Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Roman A Perez
- Bioengineering Institute of Technology, Universitat Internacional de Catalunya, Sant Cugat, Spain
| | - Alberto Perez
- The Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL, United States
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Vila-Julià G, Granadino-Roldán JM, Perez JJ, Rubio-Martinez J. Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides. J Chem Inf Model 2020; 60:1632-1643. [PMID: 31944696 DOI: 10.1021/acs.jcim.9b01047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Apoptosis is a key cell death pathway in mammalian cells. Understanding this process and its regulation has been a subject of study in the last three decades. Members of the Bcl-2 family of proteins are involved in the regulation of apoptosis through mitochondrial poration with the subsequent initiation of apoptosis. Deregulation of proapoptotic proteins contributes to the progression of many tumor processes. Understanding how these pore-forming Bcl-2 proteins Bak and Bax are activated is key to find new anticancer treatments. As no drug capable of activating Bak has been disclosed yet, the study of the structural features of BH3 peptides-known as Bak activators-relevant for binding along with its binding energy decomposition analysis, becomes essential for designing novel small-molecule mimics of BH3. Interestingly, a BH3 Bim analogue-inactivating Bak has recently been discovered, opening a question on the molecular features that determine the functions of BH3 peptides. Therefore, the present work is aimed at understanding the way BH3 peptides activate or inactivate Bak in order to identify differential structural features that can be used in drug design. For this purpose, complexes of Bak with an activator and an inhibitor have been subjected to a molecular dynamics study. Structural differences were assessed by means of the fluctuations of the corresponding principal components. Moreover, the MMPB/GBSA approach was used to compute the binding free energy of the diverse complexes to identify those residues of the BH3 peptide that exhibit the larger contributions to complex formation. The results obtained in this work show differences between activators and inhibitors, both in structural and energetic terms, which can be used in the design of new molecules that can activate or inactivate proapoptotic Bak.
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Affiliation(s)
- Guillem Vila-Julià
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028 Barcelona, Spain.,Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech., Av. Diagonal, 647, 08028 Barcelona, Spain
| | - José M Granadino-Roldán
- Departamento de Química Física y Analítica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus "Las Lagunillas" s/n, 23071 Jaén, Spain
| | - Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech., Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028 Barcelona, Spain
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Huang Z, Lu L, Jiang T, Zhang S, Shen Y, Zheng Z, Zhao A, Gao R, Li R, Zhou S, Liu J. miR-29b affects neurocyte apoptosis by targeting MCL-1 during cerebral ischemia/reperfusion injury. Exp Ther Med 2018; 16:3399-3404. [PMID: 30233687 PMCID: PMC6143871 DOI: 10.3892/etm.2018.6622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
The present study aimed to determine whether an miRNA (miR)-29b inhibitor protected against cerebral ischemia/reperfusion (I/R) injury in vitro and to investigate the underlying mechanisms. As a model for induced cerebral IR injury, N2a cells were exposed to an oxygen-glucose deprivation/reoxygenation (OGD/R) environment. Using this model, it was demonstrated that miR-29b was significantly upregulated compared with cells in a normal environment. The interactions between miR-29b and myeloid cell leukemia sequence (MCL)-1 were then investigated using dual-luciferase assays, revealing a strong regulation of MCL-1 through the 3'untranslated region. Using the OGD/R model, the present study additionally examined the effects of miR-29b and miR-29b inhibitor on cell viability and apoptosis using Cell Counting kit 8 and flow cytometry assays, respectively. miR-29b transfection led to increased N2a cell apoptosis and reduced cell viability under an OGD/R environment. However, this effect was reversed by the miR-29b inhibitor. Finally, the effects of miR-29b on the expression of several Wnt-associating proteins were examined. It was observed that B cell lymphoma-2 was inhibited by miR-29b, as was MCL-1, whereas caspase-3 expression was promoted. The miR-29b inhibitor demonstrated the opposite effect. Overall, miR-29b promoted neurocyte apoptosis by targeting MCL-1 during cerebral I/R injury. The results of the present study suggest a potential novel therapeutic target for the treatment of ischemic stroke.
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Affiliation(s)
- Zhi Huang
- Department of Intervention, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China.,Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Lu Lu
- Shenzhen Key Laboratory of Ophthalmoloy, Shenzhen Eye Hospital, Shenzhen, Guangdong 518040, P.R. China
| | - Tianpeng Jiang
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Shuai Zhang
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Yaping Shen
- Department of Intervention, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Zhu Zheng
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| | - Ansu Zhao
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| | - Rui Gao
- Guizhou Entry-Exit Inspection and Quarantine Bureau of The People's Republic of China, Guiyang, Guizhou 550002, P.R. China
| | - Rui Li
- Department of Rehabilitation, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Shi Zhou
- Department of Intervention, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China.,Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Jing Liu
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
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Perez JJ, Tomas MS, Rubio-Martinez J. Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory. J Chem Inf Model 2016; 56:1950-1962. [PMID: 27599150 DOI: 10.1021/acs.jcim.6b00347] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The goal of the present study was to ascertain the differential performance of a long molecular dynamics trajectory versus several shorter ones starting from different points in the phase space and covering the same sampling time. For this purpose, we selected the 16-mer peptide Bak16BH3 as a model for study and carried out several samplings in explicit solvent. These samplings included an 8 μs trajectory (sampling S1); two 4 μs trajectories (sampling S2); four 2 μs trajectories (sampling S3); eight 1 μs trajectories (sampling S4); 16 0.5 μs trajectories (sampling S5), and 80 0.1 μs trajectories (sampling S6). Moreover, the 8 μs trajectory was further extended to 16 μs to have reference values of the diverse properties measured. The diverse samplings were compared qualitatively and quantitatively. Among the former, we carried out a comparison of the conformational profiles of the peptide using cluster analysis. Moreover, we also gained insight into the interchange among these structures along the sampling process. Among the latter, we computed the number of new conformational patterns sampled with time using strings defined from the conformations attained by each of the residues in the peptide. We also compared the locations and depths of the obtained minima on the free energy surface using principal component analysis. Finally, we also compared the helical profiles per residue at the end of the sampling process. The results suggest that a few short molecular dynamics trajectories may provide better sampling than one unique trajectory. Moreover, this procedure can also be advantageous to avoid getting trapped in a local minimum. However, caution should be exercised since short trajectories need to be long enough to overcome local barriers surrounding the starting point and the required sampling time depends on the number of degrees of freedom of the system under study. An effective way to gain insight into the minimum MD trajectory length is to monitor the convergence of different structural features, as shown in the present work.
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Affiliation(s)
- Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya , Av. Diagonal 647, E-08028 Barcelona, Spain
| | - M Santos Tomas
- Department of Architecture Technology, Universitat Politecnica de Catalunya , Av. Diagonal 649, E-08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department of Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB) , Marti i Franques 1, E-08028 Barcelona, Spain
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