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Alvarado YJ, Olivarez Y, Lossada C, Vera-Villalobos J, Paz JL, Vera E, Loroño M, Vivas A, Torres FJ, Jeffreys LN, Hurtado-León ML, González-Paz L. Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT. Comput Biol Chem 2022; 99:107692. [PMID: 35640480 PMCID: PMC9107165 DOI: 10.1016/j.compbiolchem.2022.107692] [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: 01/04/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease Mpro. Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to Mpro. Here we show that Paxlovid binds non-covalently at regions other than the catalytic sites with energies stronger than reported and at the same binding site as the ivermectin B1a homologue, all through theoretical methodologies, including blind docking. We volumetrically characterize the non-covalent interaction of the ivermectin homologues (avermectins B1a and B1b) and Paxlovid with the mMpro monomer, through molecular dynamics and scaled particle theory (SPT). Using the fluctuation-dissipation theorem (FDT), we estimated the electric dipole moment fluctuations at the surface of each of complex involved in this study, with similar trends to that observed in the interaction volume. Using fluctuations of the intrinsic volume and the number of flexible fragments of proteins using anisotropic and Gaussian elastic networks (ANM+GNM) suggests the complexes with ivermectin are more dynamic and flexible than the unbound monomer. In contrast, the binding of Paxlovid to mMpro shows that the mMpro-PF complex is the least structurally dynamic of all the species measured in this investigation. The results support a differential molecular mechanism of the ivermectin and PF homologues in the mMpro monomer. Finally, the results showed that Paxlovid despite beingbound in different sites through covalent or non-covalent forms behaves similarly in terms of its structural flexibility and volumetric behaviour.
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Affiliation(s)
- Ysaias José Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela,Corresponding author
| | - Yosmari Olivarez
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Eddy Vera
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alejandro Vivas
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,Grupo de Química Computacional y Teórica (QCT-USFQ), Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Laura N. Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela
| | - Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela,Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela,Corresponding author at: Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela
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Kamali A, Jahmidi-Azizi N, Oliva R, Winter R. Deep sea osmolytes in action: their effect on protein-ligand binding under high pressure stress. Phys Chem Chem Phys 2022; 24:17966-17978. [PMID: 35775876 DOI: 10.1039/d2cp01769e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Because organisms living in the deep sea and in the sub-seafloor must be able to cope with hydrostatic pressures up to 1000 bar and more, their biomolecular processes, including ligand-binding reactions, must be adjusted to keep the associated volume changes low in order to function efficiently. Almost all organisms use organic cosolvents (osmolytes) to protect their cells from adverse environmental conditions. They counteract osmotic imbalance, stabilize the structure of proteins and maintain their function. We studied the binding properties of the prototypical ligand proflavine to two serum proteins with different binding pockets, BSA and HSA, in the presence of two prominent osmolytes, trimethylamine-N-oxide (TMAO) and glycine betaine (GB). TMAO and GB play an important role in the regulation and adaptation of life in deep-sea organisms. To this end, pressure dependent fluorescence spectroscopy was applied, supplemented by circular dichroism (CD) spectroscopy and computer modeling studies. The pressure-dependent measurements were also performed to investigate the intimate nature of the complex formation in relation to hydration and packing changes caused by the presence of the osmolytes. We show that TMAO and GB are able to modulate the ligand binding process in specific ways. Depending on the chemical make-up of the protein's binding pocket and thus the thermodynamic forces driving the binding process, there are osmolytes with specific interaction sites and binding strengths with water that are able to mediate efficient ligand binding even under external stress conditions. In the binding of proflavine to BSA and HSA, the addition of both compatible osmolytes leads to an increase in the binding constant upon pressurization, with TMAO being the most efficient, rendering the binding process also insensitive to pressurization even up to 2 kbar as the volume change remains close to zero. This effect can be corroborated by the effects the cosolvents impose on the strength and dynamics of hydration water as well as on the conformational dynamics of the protein.
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Affiliation(s)
- Armin Kamali
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| | - Nisrine Jahmidi-Azizi
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
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Skvarnavičius G, Toleikis Z, Matulis D, Petrauskas V. Denaturant- or ligand-induced change in protein volume by pressure shift assay. Phys Chem Chem Phys 2022; 24:17279-17288. [DOI: 10.1039/d2cp01046a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A complete thermodynamic description of protein-ligand binding includes parameters related to pressure and temperature. The changes in protein volume and compressibility upon binding a ligand are pressure-related parameters that are...
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Skvarnavičius G, Toleikis Z, Michailovienė V, Roumestand C, Matulis D, Petrauskas V. Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure. J Phys Chem B 2021; 125:5823-5831. [PMID: 34032445 PMCID: PMC8279561 DOI: 10.1021/acs.jpcb.1c02917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Proteins
undergo changes in their partial volumes in numerous biological
processes such as enzymatic catalysis, unfolding–refolding,
and ligand binding. The change in the protein volume upon ligand binding—a
parameter termed the protein–ligand binding volume—can
be extensively studied by high-pressure NMR spectroscopy. In this
study, we developed a method to determine the protein–ligand
binding volume from a single two-dimensional (2D) 1H–15N heteronuclear single quantum coherence (HSQC) spectrum
at different pressures, if the exchange between ligand-free and ligand-bound
states of a protein is slow in the NMR time-scale. This approach required
a significantly lower amount of protein and NMR time to determine
the protein–ligand binding volume of two carbonic anhydrase
isozymes upon binding their ligands. The proposed method can be used
in other protein–ligand systems and expand the knowledge about
protein volume changes upon small-molecule binding.
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Affiliation(s)
- Gediminas Skvarnavičius
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Zigmantas Toleikis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania.,Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Vilma Michailovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Christian Roumestand
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université s de Montpellier, 34000 Montpellier, France
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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Oliva R, Jahmidi-Azizi N, Mukherjee S, Winter R. Harnessing Pressure Modulation for Exploring Ligand Binding Reactions in Cosolvent Solutions. J Phys Chem B 2021; 125:539-546. [PMID: 33430595 DOI: 10.1021/acs.jpcb.0c10212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A comprehensive understanding of ligand-protein interactions requires information about all thermodynamic parameters that describe the complexation reaction, and they should be able to provide the necessary information to understand the molecular forces that drive complex formation. Usually, binding studies are performed at ambient pressure conditions. However, in addition to using temperature variation to reveal enthalpic and entropic contributions to ligand binding, complementary pressure-dependent studies providing volumetric properties of the reaction can be beneficial. Changes in partial molar volume can inform about changes in packing and hydration upon ligand binding. Here, after a general discussion of pressure effects on ligand binding reactions, we present a comprehensive study of the effect of pressure and a widely used organic cosolvent, dimethyl sulfoxide (DMSO), on the binding of a small aromatic ligand, proflavine, to the enzyme α-chymotrypsin. We found that DMSO, which acts as a competitive inhibitor for proflavine, has a strong impact on the interaction process, resulting in a decrease of the binding constant. While the reaction performed in neat buffer is basically pressure insensitive, the partial molar volume of the complex in the presence of DMSO is larger compared with the uncomplexed state, rendering the binding constant markedly smaller upon pressurization. We also show that the magnitude and sign of the binding volume provide valuable information about the interaction mechanism and hydration changes, which is of particular interest when cosolvents are present.
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Affiliation(s)
- Rosario Oliva
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Nisrine Jahmidi-Azizi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Sanjib Mukherjee
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Levin A, Cinar S, Paulus M, Nase J, Winter R, Czeslik C. Analyzing protein-ligand and protein-interface interactions using high pressure. Biophys Chem 2019; 252:106194. [PMID: 31177023 DOI: 10.1016/j.bpc.2019.106194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023]
Abstract
All protein function is based on interactions with the environment. Proteins can bind molecules for their transport, their catalytic conversion, or for signal transduction. They can bind to each other, and they adsorb at interfaces, such as lipid membranes or material surfaces. An experimental characterization is needed to understand the underlying mechanisms, but also to make use of proteins in biotechnology or biomedicine. When protein interactions are studied under high pressure, volume changes are revealed that directly describe spatial contributions to these interactions. Moreover, the strength of protein interactions with ligands or interfaces can be tuned in a smooth way by pressure modulation, which can be utilized in the design of drugs and bio-responsive interfaces. In this short review, selected studies of protein-ligand and protein-interface interactions are presented that were carried out under high pressure. Furthermore, a perspective on bio-responsive interfaces is given where protein-ligand binding is applied to create functional interfacial structures.
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Affiliation(s)
- Artem Levin
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Süleyman Cinar
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Michael Paulus
- Technische Universität Dortmund, Fakultät Physik/Delta, D-44221 Dortmund, Germany
| | - Julia Nase
- Technische Universität Dortmund, Fakultät Physik/Delta, D-44221 Dortmund, Germany
| | - Roland Winter
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Claus Czeslik
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany.
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Cinar S, Czeslik C. Inhibitor and peptide binding to calmodulin characterized by high pressure Fourier transform infrared spectroscopy and Förster resonance energy transfer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:617-623. [DOI: 10.1016/j.bbapap.2018.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
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Cinar S, Al-Ayoubi S, Sternemann C, Peters J, Winter R, Czeslik C. A high pressure study of calmodulin-ligand interactions using small-angle X-ray and elastic incoherent neutron scattering. Phys Chem Chem Phys 2018; 20:3514-3522. [PMID: 29336441 DOI: 10.1039/c7cp07399b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calmodulin (CaM) is a Ca2+ sensor and mediates Ca2+ signaling through binding of numerous target ligands. The binding of ligands by Ca2+-saturated CaM (holo-CaM) is governed by attractive hydrophobic and electrostatic interactions that are weakened under high pressure in aqueous solutions. Moreover, the potential formation of void volumes upon ligand binding creates a further source of pressure sensitivity. Hence, high pressure is a suitable thermodynamic variable to probe protein-ligand interactions. In this study, we compare the binding of two different ligands to holo-CaM as a function of pressure by using X-ray and neutron scattering techniques. The two ligands are the farnesylated hypervariable region (HVR) of the K-Ras4B protein, which is a natural binding partner of holo-CaM, and the antagonist trifluoperazine (TFP), which is known to inhibit holo-CaM activity. From small-angle X-ray scattering experiments performed up to 3000 bar, we observe a pressure-induced partial unfolding of the free holo-CaM in the absence of ligands, where the two lobes of the dumbbell-shaped protein are slightly swelled. In contrast, upon binding TFP, holo-CaM forms a closed globular conformation, which is pressure stable at least up to 3000 bar. The HVR of K-Ras4B shows a different binding behavior, and the data suggest the dissociation of the holo-CaM/HVR complex under high pressure, probably due to a less dense protein contact of the HVR as compared to TFP. The elastic incoherent neutron scattering experiments corroborate these findings. Below 2000 bar, pressure induces enhanced atomic fluctuations in both holo-CaM/ligand complexes, but those of the holo-CaM/HVR complex seem to be larger. Thus, the inhibition of holo-CaM by TFP is supported by a low-volume ligand binding, albeit this is not associated with a rigidification of the complex structure on the sub-ns Å-scale.
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Affiliation(s)
- Süleyman Cinar
- Department of Chemistry and Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany.
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Kaur A, Banipal PK, Banipal TS. Local anesthetic-bovine serum albumin interactional behaviour: Characterization by volumetric, calorimetric, and spectroscopic methods. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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