1
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Tandiana R, Barletta GP, Soler MA, Fortuna S, Rocchia W. Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔ G Predictions. J Chem Theory Comput 2024; 20:2630-2642. [PMID: 38445482 DOI: 10.1021/acs.jctc.3c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The development of highly potent antibodies and antibody fragments as binding agents holds significant implications in fields such as biosensing and biotherapeutics. Their binding strength is intricately linked to the arrangement and composition of residues at the binding interface. Computational techniques offer a robust means to predict the three-dimensional structure of these complexes and to assess the affinity changes resulting from mutations. Given the interdependence of structure and affinity prediction, our objective here is to disentangle their roles. We aim to evaluate independently six side-chain reconstruction methods and ten binding affinity estimation techniques. This evaluation was pivotal in predicting affinity alterations due to single mutations, a key step in computational affinity maturation protocols. Our analysis focuses on a data set comprising 27 distinct antibody/hen egg white lysozyme complexes, each with crystal structures and experimentally determined binding affinities. Using six different side-chain reconstruction methods, we transformed each structure into its corresponding mutant via in silico single-point mutations. Subsequently, these structures undergo minimization and molecular dynamics simulation. We therefore estimate ΔΔG values based on the original crystal structure, its energy-minimized form, and the ensuing molecular dynamics trajectories. Our research underscores the critical importance of selecting reliable side-chain reconstruction methods and conducting thorough molecular dynamics simulations to accurately predict the impact of mutations. In summary, our study demonstrates that the integration of conformational sampling and scoring is a potent approach to precisely characterizing mutation processes in single-point mutagenesis protocols and crucial for computational antibody design.
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Affiliation(s)
- Rika Tandiana
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - German P Barletta
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
- The Abdus Salam International Centre for Theoretical Physics─ICTP, Strada Costiera 11, 34151 Trieste, Italy
| | - Miguel Angel Soler
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Universita' di Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Sara Fortuna
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - Walter Rocchia
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
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2
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Ochoa R, Cossio P, Fox T. Protocol for iterative optimization of modified peptides bound to protein targets. J Comput Aided Mol Des 2022; 36:825-835. [PMID: 36258137 PMCID: PMC9640467 DOI: 10.1007/s10822-022-00482-1] [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: 07/20/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Replacing natural by non-natural amino acids can avoid these problems, and potentially improve the affinity towards the target protein. Here, we present a computational pipeline to optimize peptides based on adding non-natural amino acids while improving their binding affinity. The workflow is an iterative computational evolution algorithm, inspired by the PARCE protocol, that performs single-point mutations on the peptide sequence using modules from the Rosetta framework. The modifications can be guided based on the structural properties or previous knowledge of the biological system. At each mutation step, the affinity to the protein is estimated by sampling the complex conformations and applying a consensus metric using various open protein-ligand scoring functions. The mutations are accepted based on the score differences, allowing for an iterative optimization of the initial peptide. The sampling/scoring scheme was benchmarked with a set of protein-peptide complexes where experimental affinity values have been reported. In addition, a basic application using a known protein-peptide complex is also provided. The structure- and dynamic-based approach allows users to optimize bound peptides, with the option to personalize the code for further applications. The protocol, called mPARCE, is available at: https://github.com/rochoa85/mPARCE/.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia. .,Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany.
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia.,Center for Computational Mathematics, Flatiron Institute, New York, 10010, USA.,Center for Computational Biology, Flatiron Institute, New York, 10010, USA
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany
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3
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Nekvasilová P, Kulik N, Kotik M, Petrásková L, Slámová K, Křen V, Bojarová P. Mutation Hotspot for Changing the Substrate Specificity of β- N-Acetylhexosaminidase: A Library of GlcNAcases. Int J Mol Sci 2022; 23:12456. [PMID: 36293310 PMCID: PMC9604439 DOI: 10.3390/ijms232012456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 12/27/2023] Open
Abstract
β-N-Acetylhexosaminidase from Talaromyces flavus (TfHex; EC 3.2.1.52) is an exo-glycosidase with dual activity for cleaving N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc) units from carbohydrates. By targeting a mutation hotspot of the active site residue Glu332, we prepared a library of ten mutant variants with their substrate specificity significantly shifted towards GlcNAcase activity. Suitable mutations were identified by in silico methods. We optimized a microtiter plate screening method in the yeast Pichia pastoris expression system, which is required for the correct folding of tetrameric fungal β-N-acetylhexosaminidases. While the wild-type TfHex is promiscuous with its GalNAcase/GlcNAcase activity ratio of 1.2, the best single mutant variant Glu332His featured an 8-fold increase in selectivity toward GlcNAc compared with the wild-type. Several prepared variants, in particular Glu332Thr TfHex, had significantly stronger transglycosylation capabilities than the wild-type, affording longer chitooligomers - they behaved like transglycosidases. This study demonstrates the potential of mutagenesis to alter the substrate specificity of glycosidases.
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Affiliation(s)
- Pavlína Nekvasilová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843 Praha 2, Czech Republic
| | - Natalia Kulik
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, CZ-37333 Nové Hrady, Czech Republic
| | - Michael Kotik
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Lucie Petrásková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
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4
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Ochoa R, Lunardelli VAS, Rosa DS, Laio A, Cossio P. Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Front Immunol 2022; 13:862851. [PMID: 35572587 PMCID: PMC9094701 DOI: 10.3389/fimmu.2022.862851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Epitopes that bind simultaneously to all human alleles of Major Histocompatibility Complex class II (MHC II) are considered one of the key factors for the development of improved vaccines and cancer immunotherapies. To engineer MHC II multiple-allele binders, we developed a protocol called PanMHC-PARCE, based on the unsupervised optimization of the epitope sequence by single-point mutations, parallel explicit-solvent molecular dynamics simulations and scoring of the MHC II-epitope complexes. The key idea is accepting mutations that not only improve the affinity but also reduce the affinity gap between the alleles. We applied this methodology to enhance a Plasmodium vivax epitope for multiple-allele binding. In vitro rate-binding assays showed that four engineered peptides were able to bind with improved affinity toward multiple human MHC II alleles. Moreover, we demonstrated that mice immunized with the peptides exhibited interferon-gamma cellular immune response. Overall, the method enables the engineering of peptides with improved binding properties that can be used for the generation of new immunotherapies.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | | | - Daniela Santoro Rosa
- Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo, Sao Paulo, Brazil.,Institute for Investigation in Immunology (iii), Instituto Nacional de Ciência e Tecnologia (INCT), Sao Paulo, Brazil
| | - Alessandro Laio
- Physics Area, International School for Advanced Studies (SISSA), Trieste, Italy.,Condensed Matter and Statistical Physics Section, International Centre for Theoretical Physics (ICTP), Trieste, Italy
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Center for Computational Mathematics, Flatiron Institute, New York, NY, United States.,Center for Computational Biology, Flatiron Institute, New York, NY, United States
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5
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Pedraza-González L, Barneschi L, Padula D, De Vico L, Olivucci M. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. Top Curr Chem (Cham) 2022; 380:21. [PMID: 35291019 PMCID: PMC8924150 DOI: 10.1007/s41061-022-00374-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/29/2022] [Indexed: 10/27/2022]
Abstract
In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.
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Affiliation(s)
- Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124, Pisa, Italy.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA.
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6
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Ochoa R, Soler MA, Gladich I, Battisti A, Minovski N, Rodriguez A, Fortuna S, Cossio P, Laio A. Computational Evolution Protocol for Peptide Design. Methods Mol Biol 2022; 2405:335-359. [PMID: 35298821 DOI: 10.1007/978-1-0716-1855-4_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Computational peptide design is useful for therapeutics, diagnostics, and vaccine development. To select the most promising peptide candidates, the key is describing accurately the peptide-target interactions at the molecular level. We here review a computational peptide design protocol whose key feature is the use of all-atom explicit solvent molecular dynamics for describing the different peptide-target complexes explored during the optimization. We describe the milestones behind the development of this protocol, which is now implemented in an open-source code called PARCE. We provide a basic tutorial to run the code for an antibody fragment design example. Finally, we describe three additional applications of the method to design peptides for different targets, illustrating the broad scope of the proposed approach.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia
| | | | - Ivan Gladich
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- SISSA, Trieste, Italy
| | | | - Nikola Minovski
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - Alex Rodriguez
- The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Genova, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alessandro Laio
- The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
- SISSA, Trieste, Italy
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7
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Cantarutti C, Vargas MC, Dongmo Foumthuim CJ, Dumoulin M, La Manna S, Marasco D, Santambrogio C, Grandori R, Scoles G, Soler MA, Corazza A, Fortuna S. Insights on peptide topology in the computational design of protein ligands: the example of lysozyme binding peptides. Phys Chem Chem Phys 2021; 23:23158-23172. [PMID: 34617942 DOI: 10.1039/d1cp02536h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein, we compared the ability of linear and cyclic peptides generated in silico to target different protein sites: internal pockets and solvent-exposed sites. We selected human lysozyme (HuL) as a model target protein combined with the computational evolution of linear and cyclic peptides. The sequence evolution of these peptides was based on the PARCE algorithm. The generated peptides were screened based on their aqueous solubility and HuL binding affinity. The latter was evaluated by means of scoring functions and atomistic molecular dynamics (MD) trajectories in water, which allowed prediction of the structural features of the protein-peptide complexes. The computational results demonstrated that cyclic peptides constitute the optimal choice for solvent exposed sites, while both linear and cyclic peptides are capable of targeting the HuL pocket effectively. The most promising binders found in silico were investigated experimentally by surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and electrospray ionization mass spectrometry (ESI-MS) techniques. All tested peptides displayed dissociation constants in the micromolar range, as assessed by SPR; however, both NMR and ESI-MS suggested multiple binding modes, at least for the pocket binding peptides. A detailed NMR analysis confirmed that both linear and cyclic pocket peptides correctly target the binding site they were designed for.
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Affiliation(s)
- Cristina Cantarutti
- Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 - Udine, Italy.
| | - M Cristina Vargas
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad Mérida, Apartado Postal 73 "Cordemex", 97310, Mérida, Mexico
| | - Cedrix J Dongmo Foumthuim
- Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 - Udine, Italy. .,Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Campus Scientifico - Via Torino 155, 30172 Mestre, Italy
| | - Mireille Dumoulin
- Centre for Protein Engineering, InBios, Department of Life Sciences, University of Liege, Liege, Belgium
| | - Sara La Manna
- Department of Pharmacy - University of Naples "Federico II", 80134, Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy - University of Naples "Federico II", 80134, Naples, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Giacinto Scoles
- Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 - Udine, Italy.
| | - Miguel A Soler
- Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 - Udine, Italy. .,Italian Institute of Technology (IIT), Via Melen - 83, B Block, 16152 - Genova, Italy
| | - Alessandra Corazza
- Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 - Udine, Italy.
| | - Sara Fortuna
- Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 - Udine, Italy. .,Italian Institute of Technology (IIT), Via Melen - 83, B Block, 16152 - Genova, Italy.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
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8
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Wilson CJ, Chang M, Karttunen M, Choy WY. KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability. Int J Mol Sci 2021; 22:5408. [PMID: 34065616 PMCID: PMC8161161 DOI: 10.3390/ijms22105408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
We have performed 280 μs of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1) (G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim was to provide structural insight into the effects of these mutants, including a new class of ANCHOR (additionally NRF2-complexed hypomorph) mutant variants. Our work provides additional insight into the structural dynamics of mutants that could not be analyzed experimentally, painting a more complete picture of their mutagenic effects. Notably, blade-wise analysis of the Kelch domain points to stability as a possible target of cancer in KEAP1. Interestingly, structural analysis of the R470C ANCHOR mutant, the most prevalent missense mutation in KEAP1, revealed no significant change in structural stability or NRF2 binding site dynamics, possibly indicating an covalent modification as this mutant's mode of action.
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Affiliation(s)
- Carter J. Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
- Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
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9
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Ochoa R, Laskowski RA, Thornton JM, Cossio P. Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Front Mol Biosci 2021; 8:636562. [PMID: 34222328 PMCID: PMC8253603 DOI: 10.3389/fmolb.2021.636562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/15/2021] [Indexed: 11/23/2022] Open
Abstract
The prediction of peptide binders to Major Histocompatibility Complex (MHC) class II receptors is of great interest to study autoimmune diseases and for vaccine development. Most approaches predict the affinities using sequence-based models trained on experimental data and multiple alignments from known peptide substrates. However, detecting activity differences caused by single-point mutations is a challenging task. In this work, we used interactions calculated from simulations to build scoring matrices for quickly estimating binding differences by single-point mutations. We modelled a set of 837 peptides bound to an MHC class II allele, and optimized the sampling of the conformations using the Rosetta backrub method by comparing the results to molecular dynamics simulations. From the dynamic trajectories of each complex, we averaged and compared structural observables for each amino acid at each position of the 9°mer peptide core region. With this information, we generated the scoring-matrices to predict the sign of the binding differences. We then compared the performance of the best scoring-matrix to different computational methodologies that range in computational costs. Overall, the prediction of the activity differences caused by single mutated peptides was lower than 60% for all the methods. However, the developed scoring-matrix in combination with existing methods reports an increase in the performance, up to 86% with a scoring method that uses molecular dynamics.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Roman A Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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10
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Ochoa R, Cossio P. PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules 2021; 26:molecules26061664. [PMID: 33809815 PMCID: PMC8002403 DOI: 10.3390/molecules26061664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 11/27/2022] Open
Abstract
Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin 050010, Colombia;
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin 050010, Colombia;
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60348 Frankfurt am Main, Germany
- Correspondence:
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11
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Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. Int J Mol Sci 2021; 22:ijms22020812. [PMID: 33467468 PMCID: PMC7831021 DOI: 10.3390/ijms22020812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/17/2022] Open
Abstract
The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.
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12
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Ahmadi K, Farasat A, Rostamian M, Johari B, Madanchi H. Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study. J Biomol Struct Dyn 2021; 40:5566-5576. [PMID: 33438525 PMCID: PMC7814568 DOI: 10.1080/07391102.2021.1871958] [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] [Indexed: 01/12/2023]
Abstract
Regarding the urgency of therapeutic measures for coronavirus disease 2019 (COVID-19) pandemic, the use of available drugs with FDA approval is preferred because of the less time and cost required for their development. In silico drug repurposing is an accurate way to speed up the screening of the existing FDA-approved drugs to find a therapeutic option for COVID-19. The similarity in SARS-CoV-2 and HIV-1 fusion mechanism to host cells can be a key point for Inhibit SARS-CoV-2 entry into host cells by HIV fusion inhibitors. Accordingly, in this study, an HIV-1 fusion inhibitor called Enfuvirtide (Enf) was selected. The affinity and essential residues involving in the Enf binding to the S2 protein of SARS-CoV-2, HIV-1 gp41 protein and angiotensin-converting enzyme 2 (ACE-2) as a negative control, was evaluated using molecular docking. Eventually, Enf-S2 and Enf-gp41 protein complexes were simulated by molecular dynamics (MD) in terms of binding affinity and stability. Based on the most important criteria such as docking score, cluster size, energy and dissociation constant, the strongest interaction was observed between Enf with the S2 protein. In addition, MD results confirmed that Enf-S2 protein interaction was remarkably stable and caused the S2 protein residues to undergo the fewest fluctuations. In conclusion, it can be stated that Enf can act as a strong SARS-CoV-2 fusion inhibitor and demonstrates the potential to enter the clinical trial phase of COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Research Institute for Prevention of Non Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran.,Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Behrooz Johari
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hamid Madanchi
- Department of Biotechnology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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13
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Gheibi N, Ghorbani M, Shariatifar H, Farasat A. Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach. PLoS One 2020; 15:e0230780. [PMID: 32214349 PMCID: PMC7098580 DOI: 10.1371/journal.pone.0230780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Calprotectin is a heterodimeric protein complex with two subunits called S100A8/A9. The protein has an essential role in inflammation process and various human diseases. It has the ability to bind to unsaturated fatty acids including Arachidonic acid, Oleic acid and etc., which could be considered as a major carrier for fatty acids. In this study we aimed to appraise the thermodynamics and structural changes of Calprotectin in presence of Arachidonic acid/Oleic acid) using docking and molecular dynami simulation method. To create the best conformation of Calprotectin-Oleic acid/Arachidonic acid complexes, the docking process was performed. The complexes with the best binding energy were selected as the models for molecular dynamics simulation process. Furthermore, the structural and thermodynamics properties of the complexes were evaluated too. The Root Mean Square Deviation and Root Mean Square Fluctuation results showed that the binding of Arachidonic acid/Oleic acid to Calprotectin can cause the protein structural changes which was confirmed by Define Secondary Structure of Proteins results. Accordingly, the binding free energy results verified that binding of Oleic acid to Calprotectin leads to instability of S100A8/A9 subunits in the protein. Moreover, the electrostatic energy contribution of the complexes (Calprotectin-Oleic acid/Arachidonic acid) was remarkably higher than van der Waals energy. Thus, the outcome of this study confirm that Oleic acid has a stronger interaction with Calprotectin in comparison with Arachidonic acid. Our findings indicated that binding of unsaturated fatty acids to Calprotectin leads to structural changes of the S100A8/A9 subunits which could be beneficial to play a biological role in inflammation process.
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Affiliation(s)
- Nematollah Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohamad Ghorbani
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Hanifeh Shariatifar
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Research Institute for Prevention of Non Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
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14
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Ge C, Zhang W, He R, Cai H. Systematic Identification and Comparative Analysis of Human Cartilage-Derived Self-peptides Presented Differently by Ankylosing Spondylitis (AS)-Associated HLA-B*27:05 and Non-AS-associated HLA-B*27:09. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Gheibi N, Ghorbani M, Shariatifar H, Farasat A. In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach. PLoS One 2019; 14:e0224095. [PMID: 31622441 PMCID: PMC6797115 DOI: 10.1371/journal.pone.0224095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022] Open
Abstract
Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.
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Affiliation(s)
- Nematollah Gheibi
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Ghorbani
- Department of Nanobiotechnology/ Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Hanifeh Shariatifar
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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16
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Ochoa R, Laio A, Cossio P. Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:3464-3473. [PMID: 31290667 DOI: 10.1021/acs.jcim.9b00403] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Predicting the binding affinity of peptides able to interact with major histocompatibility complex (MHC) molecules is a priority for researchers working in the identification of novel vaccines candidates. Most available approaches are based on the analysis of the sequence of peptides of known experimental affinity. However, for MHC class II receptors, these approaches are not very accurate, due to the intrinsic flexibility of the complex. To overcome these limitations, we propose to estimate the binding affinity of peptides bound to an MHC class II by averaging the score of the configurations from finite-temperature molecular dynamics simulations. The score is estimated for 18 different scoring functions, and we explored the optimal manner for combining them. To test the predictions, we considered eight peptides of known binding affinity. We found that six scoring functions correlate with the experimental ranking of the peptides significantly better than the others. We then assessed a set of techniques for combining the scoring functions by linear regression and logistic regression. We obtained a maximum accuracy of 82% for the predicted sign of the binding affinity using a logistic regression with optimized weights. These results are potentially useful to improve the reliability of in silico protocols to design high-affinity binding peptides for MHC class II receptors.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , 050010 Medellin , Colombia
| | - Alessandro Laio
- International School for Advanced Studies (SISSA) , Via Bonomea 265 , 34136 Trieste , Italy.,The Abdus Salam International Centre for Theoretical Physics (ICTP) , Strada Costiera 11 , 34151 Trieste , Italy
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , 050010 Medellin , Colombia.,Department of Theoretical Biophysics , Max Planck Institute of Biophysics , 60438 Frankfurt am Main , Germany
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