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1.
Int J Mol Sci ; 25(7)2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38612751

ABSTRACT

The binding activity of various trastuzumab biosimilars versus the branded trastuzumab towards the glycosylated extracellular domain of the human epidermal growth factor receptor 2 (HER2) target in the presence of pertuzumab was investigated. We employed size exclusion chromatography with tetra-detection methodology to simultaneously determine absolute molecular weight, concentration, molecular size, and intrinsic viscosity. All trastuzumab molecules in solution exhibit analogous behavior in their binary action towards HER2 regardless of the order of addition of trastuzumab/pertuzumab. This analogous behavior of all trastuzumab molecules, including biosimilars, highlights the robustness and consistency of their binding activity towards HER2. Furthermore, the addition of HER2 to a mixture of trastuzumab and pertuzumab leads to increased formation of high-order HER2 complexes, up to concentrations of one order of magnitude higher than in the case of sequential addition. The observed increase suggests a potential synergistic effect between these antibodies, which could enhance their therapeutic efficacy in HER2-positive cancers. These findings underscore the importance of understanding the complex interplay between therapeutic antibodies and their target antigens, providing valuable insights for the development of more effective treatment strategies.


Subject(s)
Biosimilar Pharmaceuticals , Neoplasms , Humans , Trastuzumab/pharmacology , Trastuzumab/therapeutic use , Biosimilar Pharmaceuticals/pharmacology , Biosimilar Pharmaceuticals/therapeutic use , Antibodies, Monoclonal, Humanized/pharmacology , Antibodies, Monoclonal, Humanized/therapeutic use , Chromatography, Gel
2.
Int J Mol Sci ; 24(15)2023 Jul 27.
Article in English | MEDLINE | ID: mdl-37569408

ABSTRACT

The binding affinity of trastuzumab and pertuzumab to HER2 has been studied using both experimental and in silico methods. The experiments were conducted using the antibodies in their complete IgG form, as used in clinical therapy, and the extracellular domain of the HER2 protein in solution. This approach provides a precise, reproducible, and reliable view of the interaction between them in physicochemical conditions similar to those found in the tumoral environment. Dynamic light scattering and size exclusion chromatography coupled with tetra detection were utilized to characterize the protein complexes, measure their concentrations, and calculate the equilibrium-free binding energy, ΔGbind. In addition, PRODIGY, a QSAR-like model with excellent predictive ability, was employed to obtain in silico ΔGbind estimations. The results obtained indicate that pertuzumab exhibits a slightly higher binding affinity to HER2 than trastuzumab. The difference in binding affinity was explained based on the contribution of the different interfacial contact (IC) descriptors to the ΔGbind value estimated by the PRODIGY model. Furthermore, experiments revealed that the pertuzumab IgG antibody binds preferentially to two HER2 proteins, one per Fab fragment, while trastuzumab mainly forms a monovalent complex. This finding was interpreted based on a geometrical model that identified steric crowding in the trastuzumab-HER2 complex as compared with the pertuzumab-HER2 complex.


Subject(s)
Antibodies, Monoclonal , Receptor, ErbB-2 , Antibodies, Monoclonal, Humanized , Antineoplastic Combined Chemotherapy Protocols , Receptor, ErbB-2/metabolism , Trastuzumab
3.
J Chem Inf Model ; 61(12): 6066-6078, 2021 12 27.
Article in English | MEDLINE | ID: mdl-34874722

ABSTRACT

The AS-48 bacteriocin is a potent antimicrobial polypeptide with enhanced stability due to its circular sequence of peptidic bonds. The mechanism of biological action is still not well understood in spite of both the elucidation of the molecular structure some years ago and several experiments performed that yielded valuable information about the AS-48 bacterial membrane poration activity. In this work, we present a computational study at an atomistic scale to analyze the membrane disruption mechanism. The process is based on the two-stage model: (1) peptide binding to the bilayer surface and (2) membrane poration due to the surface tension exerted by the peptide. Indeed, the induced membrane tension mechanism is able to explain stable formation of pores leading to membrane disruption. The atomistic detail obtained from the simulations allows one to envisage the contribution of the different amino acids during the poration process. Clustering of cationic residues and hydrophobic interactions between peptide and lipids seem to be essential ingredients in the process. GLU amino acids have shown to enhance the membrane disrupting ability of the bacteriocin. TRP24-TRP24 interactions make also an important contribution in the initial stages of the poration mechanism. The detailed atomistic information obtained from the simulations can serve to better understand bacteriocin structural characteristics to design more potent antimicrobial therapies.


Subject(s)
Anti-Infective Agents , Bacteriocins , Amino Acids , Antimicrobial Cationic Peptides/chemistry , Bacteriocins/pharmacology , Lipid Bilayers/chemistry , Molecular Dynamics Simulation
4.
J Mol Model ; 22(11): 273, 2016 Nov.
Article in English | MEDLINE | ID: mdl-27783230

ABSTRACT

Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PPII and ß basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ1), along with the computation of 3J(HαHß), revealed a preference for the g - and g + rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PPII and ß basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.


Subject(s)
Oligopeptides/chemistry , Amino Acids , Nuclear Magnetic Resonance, Biomolecular , Protein Structure, Secondary
5.
J Comput Aided Mol Des ; 28(11): 1093-107, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25129484

ABSTRACT

Coarse grained (CG) modeling has been applied to study the influence of the Trastuzumab monoclonal antibody on the structure and dynamics of the full ErbB2 receptor dimer, including the lipid bilayer. The usage of CG models to study such complexes is almost mandatory, at present, due to the large size of the whole system. We will show that the Martini model performs satisfactorily well, giving results well-matched with those obtained by atomistic models as well as with the experimental information existing on homolog receptors. For example, the extra and intracellular domains approach the bilayer surface in both the monomer and dimer cases. The Trastuzumab-Fab hinders the interaction of the receptors with the lipid bilayer. Another interesting effect of the antibody is the disruption of the antiparallel arrangement of the juxtamembrane segments in the dimer case. These findings might help to understand the effect of the antibody on the receptor bioactivity.


Subject(s)
Antibodies, Monoclonal, Humanized/chemistry , Receptor, ErbB-2/chemistry , Thermodynamics , Computer Simulation , Dimerization , Lipid Bilayers/chemistry , Molecular Dynamics Simulation , Receptor, ErbB-2/drug effects , Trastuzumab
6.
Biochim Biophys Acta ; 1828(11): 2524-31, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23756777

ABSTRACT

Bacteriocin AS-48 is a membrane-interacting peptide that acts as a broad-spectrum antimicrobial against Gram-positive and Gram-negative bacteria. Prior Nuclear Magnetic Resonance experiments and the high resolution crystal structure of AS-48 have suggested a mechanism for the molecular activity of AS-48 whereby the peptide undergoes transition from a water-soluble to a membrane-bound state upon membrane binding. To help interpret experimental results, we here simulate the molecular dynamics of this binding mechanism at the coarse-grained level. By simulating the self-assembly of the peptide, we predict induction by the bacteriocin of different pore types consistent with a "leaky slit" model.


Subject(s)
Bacteriocins/metabolism , Membranes, Artificial , Bacteriocins/chemistry , Dimerization , Lipid Bilayers , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , X-Ray Diffraction
7.
J Mol Model ; 19(2): 931-41, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23090500

ABSTRACT

Epidermal growth factor receptors (EGFR) are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this work, we provide models based on homology for the extracellular domains (ECD) of ErbB3 and ErbB4 in their active conformations, including a Heregulin ligand, followed by further refinement of the models by molecular dynamics simulations at atomistic scale. We compare the results with a model built for ErbB2 based on crystallographic information and analyze the common features observed among members of the family, namely, the periscope movement of the dimerization arm and the hinge displacement of domain IV. Finally, we refine a model for the interaction of the ECDs corresponding to a ErbB2-ErbB3 heterodimer, which is widely recognized to have a high impact in cancer development.


Subject(s)
ErbB Receptors/chemistry , Molecular Dynamics Simulation , Neuregulin-1/chemistry , Receptor, ErbB-2/chemistry , Receptor, ErbB-3/chemistry , Humans , Ligands , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Structure, Secondary , Receptor, ErbB-4 , Structural Homology, Protein , Water/chemistry
8.
J Mol Model ; 19(3): 1227-36, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23160933

ABSTRACT

Human epidermal growth factor receptor 2 (ErbB2) is a transmembrane oncoprotein that is over expressed in breast cancer. A successful therapeutic treatment is a monoclonal antibody called trastuzumab which interacts with the ErbB2 extracellular domain (ErbB2-ECD). A better understanding of the detailed structure of the receptor-antibody interaction is indeed of prime interest for the design of more effective anticancer therapies. In order to discuss the flexibility of the complex ErbB2-ECD/trastuzumab, we present, in this study, a multi-nanosecond molecular dynamics simulation (MD) together with an analysis of fluctuations, through a principal component analysis (PCA) of this system. Previous to this step and in order to validate the simulations, we have performed a detailed analysis of the variable antibody domain interactions with the extracellular domain IV of ErbB2. This structure has been statically elucidated by x-ray studies. Indeed, the simulation results are in excellent agreement with the available experimental information during the full trajectory. The PCA shows eigenvector fluctuations resulting in a hinge motion in which domain II and C(H) domains approach each other. This move is likely stabilized by the formation of H-bonds and salt bridge interactions between residues of the dimerization arm in the domain II and trastuzumab residues located in the C(H) domain. Finally, we discuss the flexibility of the MD/PCA model in relation with the static x-ray structure. A movement of the antibody toward the dimerization domain of the ErbB2 receptor is reported for the first time. This finding could have important consequences on the biological action of the monoclonal antibody.


Subject(s)
Antibodies, Monoclonal, Humanized/chemistry , Antibodies, Monoclonal, Humanized/metabolism , Antineoplastic Agents/metabolism , Receptor, ErbB-2/chemistry , Receptor, ErbB-2/metabolism , Antibodies, Monoclonal, Humanized/immunology , Antineoplastic Agents/immunology , Binding Sites , Breast Neoplasms/metabolism , Female , Humans , Models, Molecular , Molecular Dynamics Simulation , Principal Component Analysis , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Receptor, ErbB-2/immunology , Trastuzumab
9.
J Mol Model ; 18(2): 515-23, 2012 Feb.
Article in English | MEDLINE | ID: mdl-21541739

ABSTRACT

In this work, the copolymerization of ethylene and methyl acrylate (MA) as catalyzed by a new Ni-based PymNox organometallic compound was studied computationally. We recently tested the behavior of this type of catalyst in ethylene homopolymerization. Experimental results show that the unsubstituted catalyst Ni2 (aldimino PymNox catalyst) is unable to incorporate the MA monomer, whereas methyl-substituted Ni1 (acetaldimino PymNox catalyst) is able to achieve copolymerization. The reactivities of both catalysts were examined using density functional theory (DFT) models. Based on energy profiles calculated at the BP86 level, a Curtin-Hammett mechanism was proposed to explain the different reactivities of the catalysts in ethylene/MA copolymerization. Our results indicate that the methyl substituent Ni1 introduces additional steric hindrance that results in a catalyst conformation that is better suited to polar monomer incorporation. This model provides insights into the design of new catalysts to produce polar functionalized copolymers based on ethylene.


Subject(s)
Acrylates/chemistry , Ethylenes/chemistry , Nickel/chemistry , Carbohydrate Conformation , Catalysis , Models, Molecular , Organometallic Compounds/chemistry , Polymerization
10.
J Phys Chem B ; 116(1): 469-75, 2012 Jan 12.
Article in English | MEDLINE | ID: mdl-22136632

ABSTRACT

The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities compare satisfactorily well with very recently published experimental data on equivalent systems. In particular, α conformation-probabilities for all of the dipeptides remain much lower than either ß or P(II) propensities. This result is in agreement with most experimental data for dipeptides. However, it is also in contrast with most simulation studies performed so far with other force fields, where α conformations result even more probable than P(II) or ß ones. We discuss the behavior of the OPLS-AA force field, which can be useful for the improvement of this model in reproducing the recent experimental observations on amino acid dipeptides.


Subject(s)
Dipeptides/chemistry , Algorithms , Amides/chemistry , Molecular Dynamics Simulation , Water/chemistry
11.
Phys Chem Chem Phys ; 13(9): 3660-8, 2011 Mar 07.
Article in English | MEDLINE | ID: mdl-21173968

ABSTRACT

Cannabinoid receptors CB1 and CB2 are a striking class of transmembrane proteins involved in a high number of important biological processes. In spite of the inherent similarity (40% in aminoacid sequence) these receptors are found in different cell environments. In addition to this, CB1 activity has been intimately associated with lipid rafts whereas CB2 has not. In this work we have performed a 50 nanosecond molecular dynamics simulation of the inactive conformations of both receptors inserted in a POPC lipid bilayer. Although in both cases the overall protein structure is maintained along the entire simulation we have found important differences in the protein-lipid interaction. While CB1 tends to distort the lipid bilayer regularity, especially in the extracellular moiety, CB2 has a minor influence on the lipid distribution along the plane of the bilayer. This observation is consistent with some experimental facts observed in these cannabinoid receptors with regard to lipid/protein interaction.


Subject(s)
Lipid Bilayers/chemistry , Molecular Dynamics Simulation , Receptor, Cannabinoid, CB1/chemistry , Receptor, Cannabinoid, CB2/chemistry , Phosphatidylcholines , Protein Interaction Domains and Motifs , Protein Structure, Tertiary , Receptor, Cannabinoid, CB1/metabolism , Receptor, Cannabinoid, CB2/metabolism
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