1. |
Cofas Vargas L. F., Olivos-Ramirez G. E., Chwastyk M.♦, Moreira R.A.♦, Baker J. L.♦, Marrink S. J.♦, Poma Bernaola A.M., Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations,
NANOSCALE, ISSN: 2040-3364, DOI: 10.1039/D4NR02074J, pp.1-11, 2024Abstract: Rational design of novel antibody therapeutics against viral infections such as coronavirus relies on surface complementarity and high affinity for their effectiveness. Here, we explore an additional property of protein complexes, the intrinsic mechanical stability, in SARS-CoV-2 variants when complexed with a potent antibody. In this study, we utilized a recent implementation of the GōMartini 3 approach to investigate large conformational changes in protein complexes with a focus on the mechanostability of the receptor-binding domain (RBD) from WT, Alpha, Delta, and XBB.1.5 variants in complex with the H11-H4 nanobody. The analysis revealed moderate differences in mechanical stability among these variants. Also, we identified crucial residues in both the RBD and certain protein segments in the nanobody that contribute to this property. By performing pulling simulations and monitoring the presence of specific native and non-native contacts across the protein complex interface, we provided mechanistic insights into the dissociation process. Force-displacement profiles indicate a tensile force clamp mechanism associated with the type of protein complex. Our computational approach not only highlights the key mechanostable interactions that are necessary to maintain overall stability, but it also paves the way for the rational design of potent antibodies that are mechanostable and effective against emergent SARS-CoV-2 variants. Keywords: SARS-CoV-2, GōMartini 3, Nanomechanics, Protein complexes, protein engineering, MD, native contacts Affiliations:
Cofas Vargas L. F. | - | IPPT PAN | Olivos-Ramirez G. E. | - | IPPT PAN | Chwastyk M. | - | Institute of Physics, Polish Academy of Sciences (PL) | Moreira R.A. | - | other affiliation | Baker J. L. | - | The College of New Jersey (US) | Marrink S. J. | - | other affiliation | Poma Bernaola A.M. | - | IPPT PAN |
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Jorge Luis M.♦, Cofas Vargas L. F., Eduardo L.♦, Jesús Antonio R.♦, Mateo C.♦, Patricia C.♦, Titaux-Delgado G.♦, Carolina Monserrath M.♦, Andrés H.♦, del Rio-Portilla F.♦, García-Hernandez E.♦, Decoding the mechanism governing the structural stability of wheat germ agglutinin and its isolated domains: A combined calorimetric, NMR, and MD simulation study,
Protein Science, ISSN: 0961-8368, DOI: 10.1002/pro.5020, Vol.33, No.6, pp.e5020-1-15, 2024Abstract: Wheat germ agglutinin (WGA) demonstrates potential as an oral delivery agent owing to its selective binding to carbohydrates and its capacity to traverse biological membranes. In this study, we employed differential scanning calorimetry and molecular dynamics simulations to comprehensively characterize the thermal unfolding process of both the complete lectin and its four isolated domains. Furthermore, we present the nuclear magnetic resonance structures of three domains that were previously lacking experimental structures in their isolated forms. Our results provide a collective understanding of the energetic and structural factors governing the intricate unfolding mechanism of the complete agglutinin, shedding light on the specific role played by each domain in this process. The analysis revealed negligible interdomain cooperativity, highlighting instead significant coupling between dimer dissociation and the unfolding of the more labile domains. By comparing the dominant interactions, we rationalized the stability differences among the domains. Understanding the structural stability of WGA opens avenues for enhanced drug delivery strategies, underscoring its potential as a promising carrier throughout the gastrointestinal environment. Keywords: homodimer, hydrogen bonding, lectin, multidomain protein, structural stability, thermal unfolding Affiliations:
Jorge Luis M. | - | other affiliation | Cofas Vargas L. F. | - | IPPT PAN | Eduardo L. | - | other affiliation | Jesús Antonio R. | - | other affiliation | Mateo C. | - | other affiliation | Patricia C. | - | other affiliation | Titaux-Delgado G. | - | other affiliation | Carolina Monserrath M. | - | other affiliation | Andrés H. | - | other affiliation | del Rio-Portilla F. | - | other affiliation | García-Hernandez E. | - | other affiliation |
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3. |
Cofas Vargas L.F., Azevedo Rodrigo M.♦, Poblete S.♦, Chwastyk M.♦, Poma Bernaola A.M.♦, The GōMartini Approach: Revisiting the Concept of Contact Maps and the Modelling of Protein Complexes,
ACTA PHYSICA POLONICA A, ISSN: 0587-4246, DOI: 10.12693/APhysPolA.145.S9, Vol.145, No.3, pp.S9-S20, 2024Abstract: We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g., distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust Gō-Martini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō--like approach to the study of protein–sugar complexes, and the limitations of this approach are also discussed. The Gō-Martini approach was first introduced by Poma et al. (J. Chem. Theory Comput. 13, 1366 (2017)) in Martini 2 force field, and recently, it has gained the status of gold standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support for this approach in the context of the biophysical community. Keywords: Martini 3,Structure-based coarse-graining,SMFS,biomolecules,GoMartini Affiliations:
Cofas Vargas L.F. | - | IPPT PAN | Azevedo Rodrigo M. | - | other affiliation | Poblete S. | - | other affiliation | Chwastyk M. | - | Institute of Physics, Polish Academy of Sciences (PL) | Poma Bernaola A.M. | - | other affiliation |
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Titaux-Delgado G.♦, Lopez-Giraldo Andrea E.♦, Carrillo E.♦, Cofas-Vargas Luis F.♦, Carranza Luis E.♦, Lopez-Vera E.♦, García-Hernandez E.♦, del Rio-Portilla F.♦, Beta-KTx14.3, a scorpion toxin, blocks the human potassium channel KCNQ1,
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, ISSN: 1570-9639, DOI: 10.1016/j.bbapap.2023.140906, Vol.1871, No.4, pp.140906-1-11, 2023Abstract: Potassium channels play a key role in regulating many physiological processes, thus, alterations in their proper functioning can lead to the development of several diseases. Hence, the search for compounds capable of regulating the activity of these channels constitutes an intense field of investigation. Potassium scorpion toxins are grouped into six subfamilies (α, β, γ, κ, δ, and λ). However, experimental structures and functional analyses of the long chain β-KTx subfamily are lacking. In this study, we recombinantly produced the toxins TcoKIK and beta-KTx14.3 present in the venom of Tityus costatus and Lychas mucronatus scorpions, respectively. The 3D structures of these β-KTx toxins were determined by nuclear magnetic resonance. In both toxins, the N-terminal region is unstructured, while the C-terminal possesses the classic CSα/β motif. TcoKIK did not show any clear activity against frog Shaker and human KCNQ1 potassium channels; however, beta-KTx14.3 was able to block the KCNQ1 channel. The toxin-channel interaction mode was investigated using molecular dynamics simulations. The results showed that this toxin could form a stable network of polar-to-polar and hydrophobic interactions with KCNQ1, involving key conserved residues in both molecular partners. The discovery and characterization of a toxin capable of inhibiting KCNQ1 pave the way for the future development of novel drugs for the treatment of human diseases caused by the malfunction of this potassium channel.
Statement of significance. Scorpion toxins have been shown to rarely block human KCNQ1 channels, which participate in the regulation of cardiac processes. In this study, we obtained recombinant beta-KTx14.3 and TcoKIK toxins and determined their 3D structures by nuclear magnetic resonance. Electrophysiological studies and molecular dynamics models were employed to examine the interactions between these two toxins and the human KCNQ1, which is the major driver channel of cardiac repolarization; beta-KTx14.3 was found to block effectively this channel. Our findings provide insights for the development of novel toxin-based drugs for the treatment of cardiac channelopathies involving KCNQ1-like channels. Keywords: β-KTx, Scorpion toxins, Cysteine-stabilized α/β motif, TcoKIK, Beta-KTx14.3, KCNQ1 Affiliations:
Titaux-Delgado G. | - | other affiliation | Lopez-Giraldo Andrea E. | - | other affiliation | Carrillo E. | - | other affiliation | Cofas-Vargas Luis F. | - | other affiliation | Carranza Luis E. | - | other affiliation | Lopez-Vera E. | - | other affiliation | García-Hernandez E. | - | other affiliation | del Rio-Portilla F. | - | other affiliation |
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Cofas-Vargas Luis F.♦, Mendoza-Espinosa P.♦, Avila-Barrientos Luis P.♦, Prada-Gracia D.♦, Riveros-Rosas H.♦, García-Hernández E.♦, Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FOF1-ATP synthase,
Frontiers in Pharmacology, ISSN: 1663-9812, DOI: 10.3389/fphar.2022.1012008, Vol.13, pp.1012008-1-19, 2022Abstract: In addition to playing a central role in the mitochondria as the main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions in the cell membrane. Its malfunction has been linked to a growing number of human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, and aging diseases. Furthermore, inhibition of this enzyme jeopardizes the survival of several bacterial pathogens of public health concern. Therefore, FOF1-ATP synthase has emerged as a novel drug target both to treat human diseases and to combat antibiotic resistance. In this work, we carried out a computational characterization of the binding sites of the fungal antibiotic aurovertin in the bovine F1 subcomplex, which shares a large identity with the human enzyme. Molecular dynamics simulations showed that although the binding sites can be described as preformed, the inhibitor hinders inter-subunit communications and exerts long-range effects on the dynamics of the catalytic site residues. End-point binding free energy calculations revealed hot spot residues for aurovertin recognition. These residues were also relevant to stabilize solvent sites determined from mixed-solvent molecular dynamics, which mimic the interaction between aurovertin and the enzyme, and could be used as pharmacophore constraints in virtual screening campaigns. To explore the possibility of finding species-specific inhibitors targeting the aurovertin binding site, we performed free energy calculations for two bacterial enzymes with experimentally solved 3D structures. Finally, an analysis of bacterial sequences was carried out to determine conservation of the aurovertin binding site. Taken together, our results constitute a first step in paving the way for structure-based development of new allosteric drugs targeting FOF1-ATP synthase sites of exogenous inhibitors. Keywords: FOF1-ATP synthase inhibition, conformational dynamics, solvent sites, binding free energy, hot spot binding residues, bacterial pathogens Affiliations:
Cofas-Vargas Luis F. | - | other affiliation | Mendoza-Espinosa P. | - | other affiliation | Avila-Barrientos Luis P. | - | other affiliation | Prada-Gracia D. | - | other affiliation | Riveros-Rosas H. | - | other affiliation | García-Hernández E. | - | other affiliation |
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6. |
Avila-Barrientos Luis P.♦, Cofas-Vargas Luis F.♦, Agüero-Chapin G.♦, García-Hernandez E.♦, Ruiz-Carmona S.♦, Valdez-Cruz Norma A.♦, Trujillo-Roldán M.♦, Weber J.♦, Ruiz-Blanco Yasser B.♦, Barril X.♦, García-Hernández E.♦, Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase,
Antibiotics, ISSN: 2079-6382, DOI: 10.3390/antibiotics11050557, Vol.11, No.5, pp.557-1-19, 2022Abstract: With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, to develop drugs with novel modes of bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as an attractive antimicrobial target, validated by the pharmaceutical approval of an inhibitor to treat multidrug-resistant tuberculosis. In this work, we aimed to design, through two types of in silico strategies, new allosteric inhibitors of the ATP synthase, by targeting the catalytic β subunit, a centerpiece in communication between rotor subunits and catalytic sites, to drive the rotary mechanism. As a model system, we used the F1 sector of Escherichia coli, a bacterium included in the priority list of multidrug-resistant pathogens. Drug-like molecules and an IF1-derived peptide, designed through molecular dynamics simulations and sequence mining approaches, respectively, exhibited in vitro micromolar inhibitor potency against F1. An analysis of bacterial and Mammalia sequences of the key structural helix-turn-turn motif of the C-terminal domain of the β subunit revealed highly and moderately conserved positions that could be exploited for the development of new species-specific allosteric inhibitors. To our knowledge, these inhibitors are the first binders computationally designed against the catalytic subunit of FOF1-ATP synthase. Keywords: FOF1-ATP synthase, allosteric inhibition, structure-based drug design, evolutionary and PPI algorithms, peptide design Affiliations:
Avila-Barrientos Luis P. | - | other affiliation | Cofas-Vargas Luis F. | - | other affiliation | Agüero-Chapin G. | - | other affiliation | García-Hernandez E. | - | other affiliation | Ruiz-Carmona S. | - | other affiliation | Valdez-Cruz Norma A. | - | other affiliation | Trujillo-Roldán M. | - | other affiliation | Weber J. | - | other affiliation | Ruiz-Blanco Yasser B. | - | other affiliation | Barril X. | - | other affiliation | García-Hernández E. | - | other affiliation |
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7. |
Labra-Núñez A.♦, Cofas-Vargas Luis F.♦, Gutiérrez-Magdaleno G.♦, Gómez-Velasco H.♦, Rodríguez-Hernández A.♦, Rodríguez-Romero A.♦, García-Hernández E.♦, Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin,
Archives of Biochemistry and Biophysics, ISSN: 0003-9861, DOI: 10.1016/j.abb.2020.108750, Vol.699, pp.108750-1-11, 2021Abstract: Bovine β-lactoglobulin, an abundant protein in whey, is a promising nanocarrier for peroral administration of drug-like hydrophobic molecules, a process that involves transit through the different acidic conditions of the human digestive tract. Among the several pH-induced conformational rearrangements that this lipocalin undergoes, the Tanford transition is particularly relevant. This transition, which occurs with a midpoint around neutral pH, involves a conformational change of the E-F loop that regulates accessibility to the primary binding site. The effect of this transition on the ligand binding properties of this protein has scarcely been explored. In this study, we carried out an energetic and structural characterization of β-lactoglobulin molecular recognition at pH values above and below the zone in which the Tanford transition occurs. The combined analysis of crystallographic, calorimetric, and molecular dynamics data sheds new light on the interplay between self-association, ligand binding, and the Tanford pre- and post-transition conformational states, revealing novel aspects underlying the molecular recognition mechanism of this enigmatic lipocalin. Keywords: Lipocalin, Structural energetics, Isothermal titration calorimetry, Molecular dynamics, X-ray crystallography Affiliations:
Labra-Núñez A. | - | other affiliation | Cofas-Vargas Luis F. | - | other affiliation | Gutiérrez-Magdaleno G. | - | other affiliation | Gómez-Velasco H. | - | other affiliation | Rodríguez-Hernández A. | - | other affiliation | Rodríguez-Romero A. | - | other affiliation | García-Hernández E. | - | other affiliation |
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8. |
Valdez Cruz Norma A.♦, García Hernández E.♦, Espitia C.♦, Cobos Marín L.♦, Altamirano C.♦, Bando Campos Carlos G.♦, Cofas-Vargas Luis F.♦, Coronado Aceves Enrique W.♦, González Hernández Ricardo A.♦, Hernández Peralta P.♦, Juárez López D.♦, Ortega Portilla Paola A.♦, Restrepo Pineda S.♦, Zelada Cordero P.♦, Trujillo Roldán Mauricio A.♦, Integrative overview of antibodies against SARS-CoV-2 and their possible applications in COVID-19 prophylaxis and treatment,
Microbial Cell Factories, ISSN: 1475-2859, DOI: 10.1186/S12934-021-01576-5, Vol.20, pp.88-1-32, 2021Abstract: SARS-CoV-2 is a novel β-coronavirus that caused the COVID-19 pandemic disease, which spread rapidly, infecting more than 134 million people, and killing almost 2.9 million thus far. Based on the urgent need for therapeutic and prophylactic strategies, the identification and characterization of antibodies has been accelerated, since they have been fundamental in treating other viral diseases. Here, we summarized in an integrative manner the present understanding of the immune response and physiopathology caused by SARS-CoV-2, including the activation of the humoral immune response in SARS-CoV-2 infection and therefore, the synthesis of antibodies. Furthermore, we also discussed about the antibodies that can be generated in COVID-19 convalescent sera and their associated clinical studies, including a detailed characterization of a variety of human antibodies and identification of antibodies from other sources, which have powerful neutralizing capacities. Accordingly, the development of effective treatments to mitigate COVID-19 is expected. Finally, we reviewed the challenges faced in producing potential therapeutic antibodies and nanobodies by cell factories at an industrial level while ensuring their quality, efficacy, and safety. Affiliations:
Valdez Cruz Norma A. | - | other affiliation | García Hernández E. | - | other affiliation | Espitia C. | - | other affiliation | Cobos Marín L. | - | other affiliation | Altamirano C. | - | other affiliation | Bando Campos Carlos G. | - | other affiliation | Cofas-Vargas Luis F. | - | other affiliation | Coronado Aceves Enrique W. | - | other affiliation | González Hernández Ricardo A. | - | other affiliation | Hernández Peralta P. | - | other affiliation | Juárez López D. | - | other affiliation | Ortega Portilla Paola A. | - | other affiliation | Restrepo Pineda S. | - | other affiliation | Zelada Cordero P. | - | other affiliation | Trujillo Roldán Mauricio A. | - | other affiliation |
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