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Reis PBPS, Clevert DA, Machuqueiro M. PypKa server: online pKa predictions and biomolecular structure preparation with precomputed data from PDB and AlphaFold DB. Nucleic Acids Res 2024; 52:W294-W298. [PMID: 38619040 PMCID: PMC11223823 DOI: 10.1093/nar/gkae255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024] Open
Abstract
When preparing biomolecular structures for molecular dynamics simulations, pKa calculations are required to provide at least a representative protonation state at a given pH value. Neglecting this step and adopting the reference protonation states of the amino acid residues in water, often leads to wrong electrostatics and nonphysical simulations. Fortunately, several methods have been developed to prepare structures considering the protonation preference of residues in their specific environments (pKa values), and some are even available for online usage. In this work, we present the PypKa server, which allows users to run physics-based, as well as ML-accelerated methods suitable for larger systems, to obtain pKa values, isoelectric points, titration curves, and structures with representative pH-dependent protonation states compatible with commonly used force fields (AMBER, CHARMM, GROMOS). The user may upload a custom structure or submit an identifier code from PBD or UniProtKB. The results for over 200k structures taken from the Protein Data Bank and the AlphaFold DB have been precomputed, and their data can be retrieved without extra calculations. All this information can also be obtained from an application programming interface (API) facilitating its usage and integration into existing pipelines as well as other web services. The web server is available at pypka.org.
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Affiliation(s)
- Pedro B P S Reis
- BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Machine Learning Research, Bayer AG, Müllerstraße 178, 13353 Berlin, Germany
| | - Djork-Arné Clevert
- Machine Learning Research, Bayer AG, Müllerstraße 178, 13353 Berlin, Germany
- Machine Learning Research, Pfizer, Berlin, Germany
| | - Miguel Machuqueiro
- BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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2
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Sandhu G, Agrawal P, Bose S, Thelma BK. Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis. J Biomol Struct Dyn 2024; 42:5912-5930. [PMID: 37378542 DOI: 10.1080/07391102.2023.2229449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
Standard force field-based simulations to accomplish structure-based evaluations of lead molecules is a powerful tool. Combining protein fragmentation into tractable sub-systems with continuum solvation method is envisaged to enable quantum mechanics-based electronic structure calculations of macromolecules in their realistic environment. This along with incorporation of many-body polarization effect in molecular dynamics simulations may augment an accurate description of electrostatics of protein-inhibitor systems for effective drug design. Rheumatoid arthritis (RA) is a complex autoimmune disorder plagued by the ceiling effect of current targeted therapies, encouraging identification of new druggable targets and corresponding drug design to tackle the refractory form of disease. In this study, polarization-inclusive force field approach has been used to model protein solvation and ligand binding for 'Mitogen-activated protein kinase' (MAP3K8), a regulatory node of notable pharmacological relevance in RA synovial biology. For MAP3K8 inhibitors belonging to different scaffold series, the calculations illustrated differential electrostatic contribution to their relative binding affinities and successfully explained examples from available structure-activity relationship studies. Results from this study exemplified i) the advantage of this approach in reliably ranking inhibitors having close nanomolar range activities for the same target; and ii) its prospective application in lead molecule identification aiding drug discovery efforts in RA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurvisha Sandhu
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
| | - Praveen Agrawal
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - Surojit Bose
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
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3
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Bosio S, Bernetti M, Rocchia W, Masetti M. Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. J Chem Inf Model 2024; 64:4570-4586. [PMID: 38800845 DOI: 10.1021/acs.jcim.4c00420] [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: 05/29/2024]
Abstract
It is nowadays clear that RNA molecules can play active roles in several biological processes. As a result, an increasing number of RNAs are gradually being identified as potentially druggable targets. In particular, noncoding RNAs can adopt highly organized conformations that are suitable for drug binding. However, RNAs are still considered challenging targets due to their complex structural dynamics and high charge density. Thus, elucidating relevant features of drug-RNA binding is fundamental for advancing drug discovery. Here, by using Molecular Dynamics simulations, we compare key features of ligand binding to proteins with those observed in RNA. Specifically, we explore similarities and differences in terms of (i) conformational flexibility of the target, (ii) electrostatic contribution to binding free energy, and (iii) water and ligand dynamics. As a test case, we examine binding of the same ligand, namely riboflavin, to protein and RNA targets, specifically the riboflavin (RF) kinase and flavin mononucleotide (FMN) riboswitch. The FMN riboswitch exhibited enhanced fluctuations and explored a wider conformational space, compared to the protein target, underscoring the importance of RNA flexibility in ligand binding. Conversely, a similar electrostatic contribution to the binding free energy of riboflavin was found. Finally, greater stability of water molecules was observed in the FMN riboswitch compared to the RF kinase, possibly due to the different shape and polarity of the pockets.
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Affiliation(s)
- Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Walter Rocchia
- Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab, Istituto Italiano di Tecnologia, Via Melen - 83, B Block, 16152 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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4
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Bosy M, Scroggs MW, Betcke T, Burman E, Cooper CD. Coupling finite and boundary element methods to solve the Poisson-Boltzmann equation for electrostatics in molecular solvation. J Comput Chem 2024; 45:787-797. [PMID: 38126925 DOI: 10.1002/jcc.27262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/03/2023] [Accepted: 11/05/2023] [Indexed: 12/23/2023]
Abstract
The Poisson-Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to the accurate representation of the molecular surface and partial charges, and exact enforcement of the boundary conditions at infinity. However, the boundary element method is limited to linear equations and piecewise constant variations of the material properties. In this work, we present a scheme that couples finite and boundary elements for the linearised Poisson-Boltzmann equation, where the finite element method is applied in a confined solute region and the boundary element method in the external solvent region. As a proof-of-concept exercise, we use the simplest methods available: Johnson-Nédélec coupling with mass matrix and diagonal preconditioning, implemented using the Bempp-cl and FEniCSx libraries via their Python interfaces. We showcase our implementation by computing the polar component of the solvation free energy of a set of molecules using a constant and a Gaussian-varying permittivity. As validation, we compare against well-established finite difference solvers for an extensive binding energy data set, and with the finite difference code APBS (to 0.5%) for Gaussian permittivities. We also show scaling results from protein G B1 (955 atoms) up to immunoglobulin G (20,148 atoms). For small problems, the coupled method was efficient, outperforming a purely boundary integral approach. For Gaussian-varying permittivities, which are beyond the applicability of boundary elements alone, we were able to run medium to large-sized problems on a single workstation. The development of better preconditioning techniques and the use of distributed memory parallelism for larger systems remains an area for future work. We hope this work will serve as inspiration for future developments that consider space-varying field parameters, and mixed linear-nonlinear schemes for molecular electrostatics with implicit solvent models.
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Affiliation(s)
- Michał Bosy
- School of Computer Science and Mathematics, Kingston University London, Kingston upon Thames, UK
| | | | - Timo Betcke
- Department of Mathematics, University College London, London, UK
| | - Erik Burman
- Department of Mathematics, University College London, London, UK
| | - Christopher D Cooper
- Department of Mechanical Engineering and Centro Científico Tecnológico de Valparaíso, Universidad Técnica Federico Santa María, Valparaíso, Chile
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5
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Rodrigues FEP, Darbre T, Machuqueiro M. High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion. J Chem Inf Model 2024; 64:3430-3442. [PMID: 38588472 DOI: 10.1021/acs.jcim.4c00018] [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: 04/10/2024]
Abstract
Peptide dendrimers are a type of branched, symmetric, and topologically well-defined molecule that have already been used as delivery systems for nucleic acid transfection. Several of the most promising sequences showed high efficiency in many key steps of transfection, namely, binding siRNA, entering cells, and evading the endosome. However, small changes to the peptide dendrimers, such as in the hydrophobic core, the amino acid chirality, or the total available charges, led to significantly different experimental results with unclear mechanistic insights. In this work, we built a computational model of several of those peptide dendrimers (MH18, MH13, and MH47) and some of their variants to study the molecular details of the structure and function of these molecules. We performed CpHMD simulations in the aqueous phase and in interaction with a lipid bilayer to assess how conformation and protonation are affected by pH in different environments. We found that while the different peptide dendrimer sequences lead to no substantial structural differences in the aqueous phase, the total charge and, more importantly, the total charge density are key for the capacity of the dendrimer to interact and destabilize the membrane. These dendrimers become highly charged when the pH changes from 7.5 to 4.5, and the presence of a high charge density, which is decreased for MH47 that has four fewer titratable lysines, is essential to trigger membrane destabilization. These findings are in excellent agreement with the experimental data and help us to understand the high efficiency of some dendrimers and why the dendrimer MH47 is unable to complete the transfection process. This evidence provides further understanding of the mode of action of these peptide dendrimers and will be pivotal for the future design of new sequences with improved transfection capabilities.
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Affiliation(s)
- Filipe E P Rodrigues
- BioISI─Instituto de Biossistemas e Ciências Integrativas Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Tamis Darbre
- Department of Chemistry Biochemistry and Pharmaceutical Sciences, University of Bern, Bern 3012, Switzerland
| | - Miguel Machuqueiro
- BioISI─Instituto de Biossistemas e Ciências Integrativas Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
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6
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Cavalieri G, Marson D, Giurgevich N, Valeri R, Felluga F, Laurini E, Pricl S. Molecular Ballet: Investigating the Complex Interaction between Self-Assembling Dendrimers and Human Serum Albumin via Computational and Experimental Methods. Pharmaceutics 2024; 16:533. [PMID: 38675194 PMCID: PMC11054399 DOI: 10.3390/pharmaceutics16040533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Dendrimers, intricate macromolecules with highly branched nanostructures, offer unique attributes including precise control over size, shape, and functionality, making them promising candidates for a wide range of biomedical applications. The exploration of their interaction with biological environments, particularly human serum albumin (HSA), holds significant importance for biomedical utilization. In this study, the interaction between HSA and a recently developed self-assembling amphiphilic dendrimer (AD) was investigated using various experimental techniques. Fluorescence spectroscopy and isothermal titration calorimetry revealed moderate interactions between the protein and the AD nanomicelles (NMs), primarily attributed to favorable enthalpic contributions arising from electrostatic interactions and hydrogen bonding. Structural analysis indicated minimal changes in HSA upon complexation with the AD NMs, which was further supported by computational simulations demonstrating stable interactions at the atomistic level. These findings provide valuable insights into the binding mechanisms and thermodynamic parameters governing HSA/AD NM interactions, thereby contributing to the understanding of their potential biomedical applications.
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Affiliation(s)
- Gabriele Cavalieri
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; (G.C.); (D.M.); (N.G.); (R.V.); (S.P.)
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; (G.C.); (D.M.); (N.G.); (R.V.); (S.P.)
| | - Nicoletta Giurgevich
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; (G.C.); (D.M.); (N.G.); (R.V.); (S.P.)
| | - Rachele Valeri
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; (G.C.); (D.M.); (N.G.); (R.V.); (S.P.)
| | - Fulvia Felluga
- Department of Chemical and Pharmaceutical Sciences, DSCF, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; (G.C.); (D.M.); (N.G.); (R.V.); (S.P.)
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; (G.C.); (D.M.); (N.G.); (R.V.); (S.P.)
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236 Łódź, Poland
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7
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Sarkar R, Mainan A, Roy S. Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods. Chem Commun (Camb) 2024. [PMID: 38501190 DOI: 10.1039/d3cc06105a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
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8
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Cherepanov DA, Milanovsky GE, Neverov KV, Obukhov YN, Maleeva YV, Aybush AV, Kritsky MS, Nadtochenko VA. Exciton interactions of chlorophyll tetramer in water-soluble chlorophyll-binding protein BoWSCP. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123847. [PMID: 38217986 DOI: 10.1016/j.saa.2024.123847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The exciton interaction of four chlorophyll a (Chl a) molecules in a symmetrical tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP was analyzed in the pH range of 3-11. Exciton splitting ΔE = 232 ± 2 cm-1 of the Qy band of Chl a into two subcomponents with relative intensities of 78.1 ± 0.7 % and 21.9 ± 0.7 % was determined by a joint decomposition of the absorption and circular dichroism spectra into Gaussian functions. The exciton coupling parameters were calculated based on the BoWSCP atomic structure in three approximations: the point dipole model, the distributed atomic monopoles, and direct ab initio calculations in the TDDFT/PCM approximation. The Coulomb interactions of monomers were calculated within the continuum model using three values of optical permittivity. The models based on the properties of free Chl a in solution suffer from significant errors both in estimating the absolute value of the exciton interaction and in the relative intensity of exciton transitions. Calculations within the TDDFT/PCM approximation reproduce the experimentally determined parameters of the exciton splitting and the relative intensities of the exciton bands. The following factors of pigment-protein and pigment-pigment interactions were examined: deviation of the macrocycle geometry from the planar conformation of free Chl; the formation of hydrogen bonds between the macrocycle and water molecules; the overlap of wave functions of monomers at close distances. The most significant factor is the geometrical deformation of the porphyrin macrocycle, which leads to an increase in the dipole moment of Chl monomer from 5.5 to 6.9 D and to a rotation of the dipole moment by 15° towards the cyclopentane ring. The contributions of resonant charge-transfer states to the wave functions of the Chl dimer were determined and the transition dipole moments of the symmetric and antisymmetric charge-transfer states were estimated.
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Affiliation(s)
- D A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation; A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Leninskye gory, 1b.40, Russian Federation.
| | - G E Milanovsky
- A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Leninskye gory, 1b.40, Russian Federation
| | - K V Neverov
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation; Faculty of Biology, Moscow State University, 119234 Moscow, Leninskye gory, 1b.12, Russian Federation
| | - Yu N Obukhov
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation
| | - Yu V Maleeva
- Faculty of Biology, Moscow State University, 119234 Moscow, Leninskye gory, 1b.12, Russian Federation
| | - A V Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation
| | - M S Kritsky
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation
| | - V A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation; Department of Chemistry, Moscow State University, 119991 Moscow, Leninskye gory, 1b.3, Russian Federation
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9
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Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. SCIENCE ADVANCES 2024; 10:eadj0384. [PMID: 38266078 PMCID: PMC10807816 DOI: 10.1126/sciadv.adj0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Proteorhodopsins are widely distributed photoreceptors from marine bacteria. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. On the basis of an integrated approach combining sensitivity-enhanced solid-state nuclear magnetic resonance (ssNMR) spectroscopy and linear-scaling quantum mechanics/molecular mechanics (QM/MM) methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shift between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation.
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Affiliation(s)
- Jiafei Mao
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - David Heidenreich
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Lynda J. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Richard C. D. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Moreno Lelli
- Department of Chemistry “Ugo Schiff” and Magnetic Resonance Center (CERM), University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- New York University–East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
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10
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Niu T, He X, Han F, Wang L, Wang J. Development and test of highly accurate endpoint free energy methods. 3: partition coefficient prediction using a Poisson-Boltzmann method combined with a solvent accessible surface area model for SAMPL challenges. Phys Chem Chem Phys 2023; 26:85-94. [PMID: 38053433 PMCID: PMC10754273 DOI: 10.1039/d3cp04174c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Accurately predicting solvation free energy is the key to predict protein-ligand binding free energy. In addition, the partition coefficient (log P), which is an important physicochemical property that determines the distribution of a drug in vivo, can be derived directly from transfer free energies, i.e., the difference between solvation free energies (SFEs) in different solvents. Within the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) 9 challenge, we applied the Poisson-Boltzmann (PB) surface area (SA) approach to predict the toluene/water transfer free energy and partition coefficient (log Ptoluene/water) from SFEs. For each solute, only a single conformation automatically generated by the free software Open Babel was used. The PB calculation directly adopts our previously optimized boundary definition - a set of general AMBER force field 2 (GAFF2) atom-type based sphere radii for solute atoms. For the non-polar SA model, we newly developed the solvent-related molecular surface tension parameters γ and offset b for toluene and cyclohexane targeting experimental SFEs. This approach yielded the highest predictive accuracy in terms of root mean square error (RMSE) of 1.52 kcal mol-1 in transfer free energy for 16 small drug molecules among all 18 submissions in the SAMPL9 blind prediction challenge. The re-evaluation of the challenge set using multi-conformation strategies based on molecular dynamics (MD) simulations further reduces the prediction RMSE to 1.33 kcal mol-1. At the same time, an additional evaluation of our PBSA method on the SAMPL5 cyclohexane/water distribution coefficient (log Dcyclohexane/water) prediction revealed that our model outperformed COSMO-RS, the best submission model with RMSEPBSA = 1.88 versus RMSECOSMO-RS = 2.11 log units. Two external log Ptoluene/water and log Pcyclohexane/water datasets that contain 110 and 87 data points, respectively, are collected for extra validation and provide an in-depth insight into the error source of the PBSA method.
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Affiliation(s)
- Taoyu Niu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Fengyang Han
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Luxuan Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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11
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Cai L, Han F, Ji B, He X, Wang L, Niu T, Zhai J, Wang J. In Silico Screening of Natural Flavonoids against 3-Chymotrypsin-like Protease of SARS-CoV-2 Using Machine Learning and Molecular Modeling. Molecules 2023; 28:8034. [PMID: 38138524 PMCID: PMC10745665 DOI: 10.3390/molecules28248034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The "Long-COVID syndrome" has posed significant challenges due to a lack of validated therapeutic options. We developed a novel multi-step virtual screening strategy to reliably identify inhibitors against 3-chymotrypsin-like protease of SARS-CoV-2 from abundant flavonoids, which represents a promising source of antiviral and immune-boosting nutrients. We identified 57 interacting residues as contributors to the protein-ligand binding pocket. Their energy interaction profiles constituted the input features for Machine Learning (ML) models. The consensus of 25 classifiers trained using various ML algorithms attained 93.9% accuracy and a 6.4% false-positive-rate. The consensus of 10 regression models for binding energy prediction also achieved a low root-mean-square error of 1.18 kcal/mol. We screened out 120 flavonoid hits first and retained 50 drug-like hits after predefined ADMET filtering to ensure bioavailability and safety profiles. Furthermore, molecular dynamics simulations prioritized nine bioactive flavonoids as promising anti-SARS-CoV-2 agents exhibiting both high structural stability (root-mean-square deviation < 5 Å for 218 ns) and low MM/PBSA binding free energy (<-6 kcal/mol). Among them, KB-2 (PubChem-CID, 14630497) and 9-O-Methylglyceofuran (PubChem-CID, 44257401) displayed excellent binding affinity and desirable pharmacokinetic capabilities. These compounds have great potential to serve as oral nutraceuticals with therapeutic and prophylactic properties as care strategies for patients with long-COVID syndrome.
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Affiliation(s)
| | | | | | | | | | | | | | - Junmei Wang
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (L.C.); (F.H.); (B.J.); (X.H.); (L.W.); (T.N.); (J.Z.)
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12
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Wilson C, Karttunen M, de Groot BL, Gapsys V. Accurately Predicting Protein p Ka Values Using Nonequilibrium Alchemy. J Chem Theory Comput 2023; 19:7833-7845. [PMID: 37820376 PMCID: PMC10653114 DOI: 10.1021/acs.jctc.3c00721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 10/13/2023]
Abstract
The stability, solubility, and function of a protein depend on both its net charge and the protonation states of its individual residues. pKa is a measure of the tendency for a given residue to (de)protonate at a specific pH. Although pKa values can be resolved experimentally, theory and computation provide a compelling alternative. To this end, we assess the applicability of a nonequilibrium (NEQ) alchemical free energy method to the problem of pKa prediction. On a data set of 144 residues that span 13 proteins, we report an average unsigned error of 0.77 ± 0.09, 0.69 ± 0.09, and 0.52 ± 0.04 pK for aspartate, glutamate, and lysine, respectively. This is comparable to current state-of-the-art predictors and the accuracy recently reached using free energy perturbation methods (e.g., FEP+). Moreover, we demonstrate that our open-source, pmx-based approach can accurately resolve the pKa values of coupled residues and observe a substantial performance disparity associated with the lysine partial charges in Amber14SB/Amber99SB*-ILDN, for which an underused fix already exists.
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Affiliation(s)
- Carter
J. Wilson
- Department
of Mathematics, The University of Western
Ontario, N6A 5B7 London, Canada
- Centre
for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, N6A 5B7 London, Canada
| | - Mikko Karttunen
- Centre
for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, N6A 5B7 London, Canada
- Department
of Physics & Astronomy, The University
of Western Ontario, N6A
5B7 London, Canada
- Department
of Chemistry, The University of Western
Ontario, N6A 5B7 London, Canada
| | - Bert L. de Groot
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, 37077 Göttingen, Germany
| | - Vytautas Gapsys
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, 37077 Göttingen, Germany
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
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13
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Ge H, Ji B, Fang J, Wang J, Li J, Wang J. Discovery of Potent and Selective CB2 Agonists Utilizing a Function-Based Computational Screening Protocol. ACS Chem Neurosci 2023; 14:3941-3958. [PMID: 37823773 PMCID: PMC10623575 DOI: 10.1021/acschemneuro.3c00580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
Nowadays, the identification of agonists and antagonists represents a great challenge in computer-aided drug design. In this work, we developed a computational protocol enabling us to design/screen novel chemicals that are likely to serve as selective CB2 agonists. The principle of this protocol is that by calculating the ligand-residue interaction profile (LRIP) of a ligand binding to a specific target, the agonist-antagonist function of a compound is then able to be determined after statistical analysis and free energy calculations. This computational protocol was successfully applied in CB2 agonist development starting from a lead compound, and a success rate of 70% was achieved. The functions of the synthesized derivatives were determined by in vitro functional assays. Moreover, the identified potent CB2 agonists and antagonists strongly interact with the key residues identified using the already known potent CB2 agonists/antagonists. The analysis of the interaction profile of compound 6, a potent agonist, showed strong interactions with F2.61, I186, and F2.64, while compound 39, a potent antagonist, showed strong interactions with L17, W6.48, V6.51, and C7.42. Still, some residues including V3.32, T3.33, S7.39, F183, W5.43, and I3.29 are hotspots for both CB2 agonists and antagonists. More significantly, we identified three hotspot residues in the loop, including I186 for agonists, L17 for antagonists, and F183 for both. These hotspot residues are typically not considered in CB1/CB2 rational ligand design. In conclusion, LRIP is a useful concept in rationally designing a compound to possess a certain function.
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Affiliation(s)
- Haixia Ge
- School
of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Beihong Ji
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jiahui Fang
- Chinese
Academy of Sciences Key Laboratory of Receptor Research, National
Center for Drug Screening, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiayang Wang
- School
of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Jing Li
- Chinese
Academy of Sciences Key Laboratory of Receptor Research, National
Center for Drug Screening, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Junmei Wang
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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14
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Yepuri G, Ramirez LM, Theophall GG, Reverdatto SV, Quadri N, Hasan SN, Bu L, Thiagarajan D, Wilson R, Díez RL, Gugger PF, Mangar K, Narula N, Katz SD, Zhou B, Li H, Stotland AB, Gottlieb RA, Schmidt AM, Shekhtman A, Ramasamy R. DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress. Nat Commun 2023; 14:6900. [PMID: 37903764 PMCID: PMC10616211 DOI: 10.1038/s41467-023-42521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
Inter-organelle contact and communication between mitochondria and sarco/endoplasmic reticulum (SR/ER) maintain cellular homeostasis and are profoundly disturbed during tissue ischemia. We tested the hypothesis that the formin Diaphanous-1 (DIAPH1), which regulates actin dynamics, signal transduction and metabolic functions, contributes to these processes. We demonstrate that DIAPH1 interacts directly with Mitofusin-2 (MFN2) to shorten mitochondria-SR/ER distance, thereby enhancing mitochondria-ER contact in cells including cardiomyocytes, endothelial cells and macrophages. Solution structure studies affirm the interaction between the Diaphanous Inhibitory Domain and the cytosolic GTPase domain of MFN2. In male rodent and human cardiomyocytes, DIAPH1-MFN2 interaction regulates mitochondrial turnover, mitophagy, and oxidative stress. Introduction of synthetic linker construct, which shorten the mitochondria-SR/ER distance, mitigated the molecular and functional benefits of DIAPH1 silencing in ischemia. This work establishes fundamental roles for DIAPH1-MFN2 interaction in the regulation of mitochondria-SR/ER contact networks. We propose that targeting pathways that regulate DIAPH1-MFN2 interactions may facilitate recovery from tissue ischemia.
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Affiliation(s)
- Gautham Yepuri
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Lisa M Ramirez
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Gregory G Theophall
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Sergei V Reverdatto
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Nosirudeen Quadri
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Syed Nurul Hasan
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Lei Bu
- Department of Medicine, Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Devi Thiagarajan
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Robin Wilson
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Raquel López Díez
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Paul F Gugger
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Kaamashri Mangar
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Navneet Narula
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Stuart D Katz
- Department of Medicine, Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Boyan Zhou
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Huilin Li
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Aleksandr B Stotland
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Roberta A Gottlieb
- Department of Biomedical Sciences, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Alexander Shekhtman
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Ravichandran Ramasamy
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA.
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15
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Chakraborty G, Nath I V A, Sharma M, Sheth J, Kori M, Tiwari A, Patra N. In silico structural and mechanical insights into bedaquiline resistance associated with high-grade non-synonymous mutations in atpE, mmpR5, and pepQ. J Biomol Struct Dyn 2023:1-13. [PMID: 37728541 DOI: 10.1080/07391102.2023.2259486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Clinical resistance against bedaquiline (BDQ) remains intractable to anti-tuberculosis therapies since its introduction to the market over a decade ago. Herein, we investigated the structural and mechanical aspects of BDQ resistance in AtpE, MmpR5, and PepQ. The known target-specific resistant single non-synonymous mutations were refined to high-grade candidates. Thus, 7 (AtpE), 5 (MmpR5), and 1 (PepQ) single nucleotide polymorphisms (SNPs) and one insertion frameshift mutation in MmpR5 were recreated at the molecular level, and these phenotypic models were then directed to stringent dynamics to define time-scaled changes. The AtpE variants destabilized the structure; mainly, L59V, E61D, and I66M were detrimental to the complex fitness, while L74V and L114P boosted the BDQ binding to MmpR5. The first three and last two alterations gave rise to loss- and gain-of-function to AtpE and MmpR5, respectively. Hence, these five mutants are functionally relevant and therapeutically targetable hotspots of BDQ resistance. There were no noticeable changes in PepQ data analysis. The present study revealed that MmpR5 mutations confer BDQ resistance, whereas AtpE and PepQ SNPs display low susceptibility. These results were tallied with the published findings, which testified to the pursued method's reliability and accuracy. We hope these data and inferences could be helpful for the futuristic design of novel TB drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Mukta Sharma
- AarogyaAI Innovations Private Limited, Bengaluru, India
| | - Jigar Sheth
- AarogyaAI Innovations Private Limited, Bengaluru, India
| | - Mahima Kori
- AarogyaAI Innovations Private Limited, Bengaluru, India
| | | | - Niladri Patra
- Indian Institute of Technology (Indian School of Mines), Dhanbad, India
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16
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Sun Y, Hou T, He X, Man VH, Wang J. Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method. J Comput Chem 2023; 44:1300-1311. [PMID: 36820817 PMCID: PMC10101867 DOI: 10.1002/jcc.27086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/16/2022] [Accepted: 01/29/2023] [Indexed: 02/24/2023]
Abstract
The logarithm of n-octanol-water partition coefficient (logP) is frequently used as an indicator of lipophilicity in drug discovery, which has substantial impacts on the absorption, distribution, metabolism, excretion, and toxicity of a drug candidate. Considering that the experimental measurement of the property is costly and time-consuming, it is of great importance to develop reliable prediction models for logP. In this study, we developed a transfer free energy-based logP prediction model-FElogP. FElogP is based on the simple principle that logP is determined by the free energy change of transferring a molecule from water to n-octanol. The underlying physical method to calculate transfer free energy is the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), thus this method is named as free energy-based logP (FElogP). The superiority of FElogP model was validated by a large set of 707 structurally diverse molecules in the ZINC database for which the measurement was of high quality. Encouragingly, FElogP outperformed several commonly-used QSPR or machine learning-based logP models, as well as some continuum solvation model-based methods. The root-mean-square error (RMSE) and Pearson correlation coefficient (R) between the predicted and measured values are 0.91 log units and 0.71, respectively, while the runner-up, the logP model implemented in OpenBabel had an RMSE of 1.13 log units and R of 0.67. Given the fact that FElogP was not parameterized against experimental logP directly, its excellent performance is likely to be expanded to arbitrary organic molecules covered by the general AMBER force fields.
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Affiliation(s)
- Yuchen Sun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
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17
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Awoonor-Williams E, Golosov AA, Hornak V. Benchmarking In Silico Tools for Cysteine p Ka Prediction. J Chem Inf Model 2023; 63:2170-2180. [PMID: 36996330 DOI: 10.1021/acs.jcim.3c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Accurate estimation of the pKa's of cysteine residues in proteins could inform targeted approaches in hit discovery. The pKa of a targetable cysteine residue in a disease-related protein is an important physiochemical parameter in covalent drug discovery, as it influences the fraction of nucleophilic thiolate amenable to chemical protein modification. Traditional structure-based in silico tools are limited in their predictive accuracy of cysteine pKa's relative to other titratable residues. Additionally, there are limited comprehensive benchmark assessments for cysteine pKa predictive tools. This raises the need for extensive assessment and evaluation of methods for cysteine pKa prediction. Here, we report the performance of several computational pKa methods, including single-structure and ensemble-based approaches, on a diverse test set of experimental cysteine pKa's retrieved from the PKAD database. The dataset consisted of 16 wildtype and 10 mutant proteins with experimentally measured cysteine pKa values. Our results highlight that these methods are varied in their overall predictive accuracies. Among the test set of wildtype proteins evaluated, the best method (MOE) yielded a mean absolute error of 2.3 pK units, highlighting the need for improvement of existing pKa methods for accurate cysteine pKa estimation. Given the limited accuracy of these methods, further development is needed before these approaches can be routinely employed to drive design decisions in early drug discovery efforts.
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Affiliation(s)
- Ernest Awoonor-Williams
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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18
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Yousaf N, Jabeen Y, Imran M, Saleem M, Rahman M, Maqbool A, Iqbal M, Muddassar M. Exploiting the co-crystal ligands shape, features and structure-based approaches for identification of SARS-CoV-2 Mpro inhibitors. J Biomol Struct Dyn 2023; 41:14325-14338. [PMID: 36946192 DOI: 10.1080/07391102.2023.2189478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/08/2023] [Indexed: 03/23/2023]
Abstract
SARS-CoV-2 enters the host cell through the ACE2 receptor and replicates its genome using an RNA-Dependent RNA Polymerase (RDRP). The functional RDRP is released from pro-protein pp1ab by the proteolytic activity of Main protease (Mpro) which is encoded within the viral genome. Due to its vital role in proteolysis of viral polyprotein chains, it has become an attractive potential drug target. We employed a hierarchical virtual screening approach to identify small synthetic protease inhibitors. Statistically optimized molecular shape and color-based features (various functional groups) from co-crystal ligands were used to screen different databases through various scoring schemes. Then, the electrostatic complementarity of screened compounds was matched with the most active molecule to further reduce the hit molecules' size. Finally, five hundred eighty-seven molecules were docked in Mpro catalytic binding site, out of which 29 common best hits were selected based on Glide and FRED scores. Five best-fitting compounds in complex with Mpro were subjected to MD simulations to analyze their structural stability and binding affinities with Mpro using MM/GB(PB)SA models. Modeling results suggest that identified hits can act as the lead compounds for designing better active Mpro inhibitors to enhance the chemical space to combat COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Numan Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Yaruq Jabeen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Imran
- KAM School of Life Sciences, Forman Christian College, Lahore, Pakistan
| | - Muhammad Saleem
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Moazur Rahman
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Abbas Maqbool
- Department of Biochemistry and Metabolism John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mazhar Iqbal
- Health Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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19
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Sun Y, He X, Hou T, Cai L, Man VH, Wang J. Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method. J Comput Chem 2023; 44:1334-1346. [PMID: 36807356 DOI: 10.1002/jcc.27089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/22/2022] [Accepted: 01/29/2023] [Indexed: 02/23/2023]
Abstract
Accurate estimation of solvation free energy (SFE) lays the foundation for accurate prediction of binding free energy. The Poisson-Boltzmann (PB) or generalized Born (GB) combined with surface area (SA) continuum solvation method (PBSA and GBSA) have been widely used in SFE calculations because they can achieve good balance between accuracy and efficiency. However, the accuracy of these methods can be affected by several factors such as the charge models, polar and nonpolar SFE calculation methods and the atom radii used in the calculation. In this work, the performance of the ABCG2 (AM1-BCC-GAFF2) charge model as well as other two charge models, that is, RESP (Restrained Electrostatic Potential) and AM1-BCC (Austin Model 1-bond charge corrections), on the SFE prediction of 544 small molecules in water by PBSA/GBSA was evaluated. In order to improve the performance of the PBSA prediction based on the ABCG2 charge, we further explored the influence of atom radii on the prediction accuracy and yielded a set of atom radius parameters for more accurate SFE prediction using PBSA based on the ABCG2/GAFF2 by reproducing the thermodynamic integration (TI) calculation results. The PB radius parameters of carbon, oxygen, sulfur, phosphorus, chloride, bromide and iodine, were adjusted. New atom types, on, oi, hn1, hn2, hn3, were introduced to further improve the fitting performance. Then, we tuned the parameters in the nonpolar SFE model using the experimental SFE data and the PB calculation results. By adopting the new radius parameters and new nonpolar SFE model, the root mean square error (RMSE) of the SFE calculation for the 544 molecules decreased from 2.38 to 1.05 kcal/mol. Finally, the new radius parameters were applied in the prediction of protein-ligand binding free energies using the MM-PBSA method. For the eight systems tested, we could observe higher correlation between the experiment data and calculation results and smaller prediction errors for the absolute binding free energies, demonstrating that our new radius parameters can improve the free energy calculation using the MM-PBSA method.
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Affiliation(s)
- Yuchen Sun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lianjin Cai
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Viet Hoag Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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20
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Jiang C, He X, Wang Y, Chen CJ, Othman Y, Hao Y, Yuan J, Xie XQ, Feng Z. Molecular Modeling Study of a Receptor-Orthosteric Ligand-Allosteric Modulator Signaling Complex. ACS Chem Neurosci 2023; 14:418-434. [PMID: 36692197 PMCID: PMC10032570 DOI: 10.1021/acschemneuro.2c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Allosteric modulators (AMs) are considered as a perpetual hotspot in research for their higher selectivity and various effects on orthosteric ligands (OL). They are classified in terms of their functionalities as positive, negative, or silent allosteric modulators (PAM, NAM, or SAM, respectively). In the present work, 11 pairs of three-dimensional (3D) structures of receptor-orthosteric ligand and receptor-orthosteric ligand-allosteric modulator complexes have been collected for the studies, including three different systems: GPCR, enzyme, and ion channel. Molecular dynamics (MD) simulations are applied to quantify the dynamic interactions in both the orthosteric and allosteric binding pockets and the structural fluctuation of the involved proteins. Our results showed that MD simulations of moderately large molecules or peptides undergo insignificant changes compared to crystal structure results. Furthermore, we also studied the conformational changes of receptors that bound with PAM and NAM, as well as the different allosteric binding sites in a receptor. There should be no preference for the position of the allosteric binding pocket after comparing the allosteric binding pockets of these three systems. Finally, we aligned four distinct β2 adrenoceptor structures and three N-methyl-d-aspartate receptor (NMDAR) structures to investigate conformational changes. In the β2 adrenoceptor systems, the aligned results revealed that transmembrane (TM) helices 1, 5, and 6 gradually increased outward movement from an enhanced inactive state to an improved active state. TM6 endured the most significant conformational changes (around 11 Å). For NMDAR, the bottom section of NMDAR's ligand-binding domain (LBD) experienced an upward and outward shift during the gradually activating process. In conclusion, our research provides insight into receptor-orthosteric ligand-allosteric modulator studies and the design and development of allosteric modulator drugs using MD simulation.
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Affiliation(s)
- Chen Jiang
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Xibing He
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Yuanqiang Wang
- School
of Pharmacy and Bioengineering, Chongqing
University of Technology, Chongqing400054, China
- Chongqing
Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing400054, China
- Chongqing
Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing400054, China
| | - Chih-Jung Chen
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Yasmin Othman
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Yixuan Hao
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Jiayi Yuan
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Xiang-Qun Xie
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Zhiwei Feng
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
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21
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Wan Z, Huang H, West RE, Zhang M, Zhang B, Cai X, Zhang Z, Luo Z, Chen Y, Zhang Y, Xie W, Yang D, Nolin TD, Wang J, Li S, Sun J. Overcoming pancreatic cancer immune resistance by codelivery of CCR2 antagonist using a STING-activating gemcitabine-based nanocarrier. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2023; 62:33-50. [PMID: 38239407 PMCID: PMC10795849 DOI: 10.1016/j.mattod.2022.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
STING agonist has recently gained much attention for cancer treatment, but the therapeutic potential of STING agonist is hampered by STING-associated tumor immune resistance. In this work, guided by both bioinformatics and computer modeling, we rationally designed a "one stone hits two birds" nanoparticle-based strategy to simultaneously activate STING innate immune response while eliminating STING-associated immune resistance for the treatment of pancreatic ductal adenocarcinoma (PDAC). We discovered that the ultra-small sized micellar system based on gemcitabine-conjugated polymer (PGEM), which showed superior capacity of penetration in pancreatic tumor spheroid model and orthotopic tumor model, could serve as a novel "STING agonist". The activation of STING signaling in dendritic cells (DCs) by PGEM increased both innate nature killer (NK) and adaptive anti-tumor T cell response. However, activation of STING signaling by PGEM in tumor cells also drove the induction of chemokines CCL2 and CCL7, resulting in immune resistance by recruiting tumor associated macrophage (TAM) and myeloid-derived suppressor cells (MDSCs). Through the combination of computer modeling and experimental screening, we developed a dual delivery modality by incorporating a CCR2 (the receptor shared by both CCL2 and CCL7) antagonist PF-6309 (PF) into PGEM micellar system. Our studies demonstrated that PGEM/PF formulation significantly reduced pancreatic tumor burden and induced potent anti-tumor immunity through reversing the CCL2/CCL7-mediated immunosuppression. Moreover, PGEM/PF sensitized PDAC tumors to anti-PD-1 therapy, leading to complete suppression/eradication of the tumors. Our work has shed light to the multi-faceted role of STING activation and provided a novel immunotherapy regimen to maximize the benefit of STING activation for PDAC treatment. In addition, this work paved a new way for bioinformatics and computer modeling-guided rational design of nanomedicine.
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Affiliation(s)
- Zhuoya Wan
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Haozhe Huang
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Raymond E West
- Department of Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Bei Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Xinran Cai
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Ziqian Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Zhangyi Luo
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Yuang Chen
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Yue Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Wen Xie
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Thomas D Nolin
- Department of Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Jingjing Sun
- Center for Pharmacogenetics, Department of Pharmaceutical Science, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
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22
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Investigation of the Fuzzy Complex between RSV Nucleoprotein and Phosphoprotein to Optimize an Inhibition Assay by Fluorescence Polarization. Int J Mol Sci 2022; 24:ijms24010569. [PMID: 36614009 PMCID: PMC9820559 DOI: 10.3390/ijms24010569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
The interaction between Respiratory Syncytial Virus phosphoprotein P and nucleoprotein N is essential for the formation of the holo RSV polymerase that carries out replication. In vitro screening of antivirals targeting the N-P protein interaction requires a molecular interaction model, ideally consisting of a complex between N protein and a short peptide corresponding to the C-terminal tail of the P protein. However, the flexibility of C-terminal P peptides as well as their phosphorylation status play a role in binding and may bias the outcome of an inhibition assay. We therefore investigated binding affinities and dynamics of this interaction by testing two N protein constructs and P peptides of different lengths and composition, using nuclear magnetic resonance and fluorescence polarization (FP). We show that, although the last C-terminal Phe241 residue is the main determinant for anchoring P to N, only longer peptides afford sub-micromolar affinity, despite increasing mobility towards the N-terminus. We investigated competitive binding by peptides and small compounds, including molecules used as fluorescent labels in FP. Based on these results, we draw optimized parameters for a robust RSV N-P inhibition assay and validated this assay with the M76 molecule, which displays antiviral properties, for further screening of chemical libraries.
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23
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Siryk S, Rocchia W. Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson-Boltzmann Framework: An Analytical Treatment. J Phys Chem B 2022; 126:10400-10426. [PMID: 36473089 PMCID: PMC9761689 DOI: 10.1021/acs.jpcb.2c05564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This work considers the interaction of two dielectric particles of arbitrary shape immersed into a solvent containing a dissociated salt and assuming that the linearized Poisson-Boltzmann equation holds. We establish a new general spherical re-expansion result which relies neither on the conventional condition that particle radii are small with respect to the characteristic separating distance between particles nor on any symmetry assumption. This is instrumental in calculating suitable expansion coefficients for the electrostatic potential inside and outside the objects and in constructing small-parameter asymptotic expansions for the potential, the total electrostatic energy, and forces in ascending order of Debye screening. This generalizes a recent result for the case of dielectric spheres to particles of arbitrary shape and builds for the first time a rigorous (exact at the Debye-Hückel level) analytical theory of electrostatic interactions of such particles at arbitrary distances. Numerical tests confirm that the proposed theory may also become especially useful in developing a new class of grid-free, fast, highly scalable solvers.
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24
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Yang S, Tang Y, Liu Y, Brown AJ, Schaks M, Ding B, Kramer DA, Mietkowska M, Ding L, Alekhina O, Billadeau DD, Chowdhury S, Wang J, Rottner K, Chen B. Arf GTPase activates the WAVE regulatory complex through a distinct binding site. SCIENCE ADVANCES 2022; 8:eadd1412. [PMID: 36516255 PMCID: PMC9750158 DOI: 10.1126/sciadv.add1412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/10/2022] [Indexed: 06/02/2023]
Abstract
Cross-talk between Rho- and Arf-family guanosine triphosphatases (GTPases) plays an important role in linking the actin cytoskeleton to membrane protrusions, organelle morphology, and vesicle trafficking. The central actin regulator, WAVE regulatory complex (WRC), integrates Rac1 (a Rho-family GTPase) and Arf signaling to promote Arp2/3-mediated actin polymerization in many processes, but how WRC senses Arf signaling is unknown. Here, we have reconstituted a direct interaction between Arf and WRC. This interaction is greatly enhanced by Rac1 binding to the D site of WRC. Arf1 binds to a previously unidentified, conserved surface on the Sra1 subunit of WRC, which, in turn, drives WRC activation using a mechanism distinct from that of Rac1. Mutating the Arf binding site abolishes Arf1-WRC interaction, disrupts Arf1-mediated WRC activation, and impairs lamellipodia formation and cell migration. This work uncovers a new mechanism underlying WRC activation and provides a mechanistic foundation for studying how WRC-mediated actin polymerization links Arf and Rac signaling in cells.
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Affiliation(s)
- Sheng Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Yubo Tang
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Yijun Liu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Abbigale J. Brown
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Matthias Schaks
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Bojian Ding
- Department of Biochemistry and Cell Biology, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794, USA
| | - Daniel A. Kramer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Magdalena Mietkowska
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Li Ding
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN 55905, USA
| | - Olga Alekhina
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN 55905, USA
| | - Daniel D. Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN 55905, USA
| | - Saikat Chowdhury
- Department of Biochemistry and Cell Biology, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794, USA
- CSIR–Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, 3501 Terrace St., Pittsburgh, PA 15261, USA
| | - Klemens Rottner
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
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25
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Ruiz-Rodríguez MA, Cooper CD, Rocchia W, Casalegno M, López de los Santos Y, Raos G. Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode. J Phys Chem B 2022; 126:8777-8790. [PMID: 36269122 PMCID: PMC9639099 DOI: 10.1021/acs.jpcb.2c05371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrogenases are a group of enzymes that have caught the interest of researchers in renewable energies, due to their ability to catalyze the redox reaction of hydrogen. The exploitation of hydrogenases in electrochemical devices requires their immobilization on the surface of suitable electrodes, such as graphite. The orientation of the enzyme on the electrode is important to ensure a good flux of electrons to the catalytic center, through an array of iron-sulfur clusters. Here we present a computational approach to determine the possible orientations of a [NiFe] hydrogenase (PDB 1e3d) on a planar electrode, as a function of pH, salinity, and electrode potential. The calculations are based on the solution of the linearized Poisson-Boltzmann equation, using the PyGBe software. The results reveal that electrostatic interactions do not truly immobilize the enzyme on the surface of the electrode, but there is instead a dynamic equilibrium between different orientations. Nonetheless, after averaging over all thermally accessible orientations, we find significant differences related to the solution's salinity and pH, while the effect of the electrode potential is relatively weak. We also combine models for the protein adsoption-desorption equilibria and for the electron transfer between the proteins and the electrode to arrive at a prediction of the electrode's activity as a function of the enzyme concentration.
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Affiliation(s)
| | - Christopher D. Cooper
- Department
of Mechanical Engineering and Centro Científico Tecnológico
de Valparaíso, Universidad Técnica
Federico Santa María, Valparaíso, 2340000, Chile
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, 16163Genova, Italy
| | - Mosè Casalegno
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy
| | - Yossef López de los Santos
- Centre
Armand-Frappier Santé, Biotechnologie, Institut national de
la recherche scientifique (INRS), Université
du Québec, Laval, QuébecHV7 1B7, Canada
| | - Guido Raos
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy,
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26
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Tam JZ, Palumbo T, Miwa JM, Chen BY. Analysis of Protein-Protein Interactions for Intermolecular Bond Prediction. Molecules 2022; 27:molecules27196178. [PMID: 36234723 PMCID: PMC9572624 DOI: 10.3390/molecules27196178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/03/2022] [Accepted: 09/10/2022] [Indexed: 11/24/2022] Open
Abstract
Protein-protein interactions often involve a complex system of intermolecular interactions between residues and atoms at the binding site. A comprehensive exploration of these interactions can help reveal key residues involved in protein-protein recognition that are not obvious using other protein analysis techniques. This paper presents and extends DiffBond, a novel method for identifying and classifying intermolecular bonds while applying standard definitions of bonds in chemical literature to explain protein interactions. DiffBond predicted intermolecular bonds from four protein complexes: Barnase-Barstar, Rap1a-raf, SMAD2-SMAD4, and a subset of complexes formed from three-finger toxins and nAChRs. Based on validation through manual literature search and through comparison of two protein complexes from the SKEMPI dataset, DiffBond was able to identify intermolecular ionic bonds and hydrogen bonds with high precision and recall, and identify salt bridges with high precision. DiffBond predictions on bond existence were also strongly correlated with observations of Gibbs free energy change and electrostatic complementarity in mutational experiments. DiffBond can be a powerful tool for predicting and characterizing influential residues in protein-protein interactions, and its predictions can support research in mutational experiments and drug design.
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Affiliation(s)
- Justin Z. Tam
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Talulla Palumbo
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Julie M. Miwa
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Brian Y. Chen
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
- Correspondence:
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27
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Folescu DE, Onufriev AV. A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules. ACS OMEGA 2022; 7:26123-26136. [PMID: 35936397 PMCID: PMC9352323 DOI: 10.1021/acsomega.2c01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value as these can provide computational speed, versatility, and physical insight. Here, we have derived a simple, closed-form formula for the apparent surface charge (ASC) as well as for the electric field generated by a molecular charge distribution in aqueous solution. The approximation, with no fitted parameters, was tested against numerical solutions of the Poisson equation, where it has produced a significant speed-up. For neutral small molecules, the hydration free energies estimated from the closed-form ASC formula are within 0.8 kcal/mol RMSD from the numerical Poisson reference; the electric field at the surface is in quantitative agreement with the reference. Performance of the approximation was also tested on larger structures, including a protein, a DNA fragment, and a viral receptor-target complex. For all structures tested, a near-quantitative agreement with the numerical Poisson reference was achieved, except in regions of high negative curvature, where the new approximation is still qualitatively correct. A unique efficiency feature of the proposed "source-based″ closed-form approximation is that the ASC and electric field can be estimated individually at any point or surface patch, without the need to obtain the full global solution. An open-source software implementation of the method is available: https://people.cs.vt.edu/~onufriev/CODES/aasc.zip.
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Affiliation(s)
- Dan E. Folescu
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexey V. Onufriev
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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28
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Reis PBPS, Bertolini M, Montanari F, Rocchia W, Machuqueiro M, Clevert DA. A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven p Ka Predictions in Proteins. J Chem Theory Comput 2022; 18:5068-5078. [PMID: 35837736 DOI: 10.1021/acs.jctc.2c00308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Existing computational methods for estimating pKa values in proteins rely on theoretical approximations and lengthy computations. In this work, we use a data set of 6 million theoretically determined pKa shifts to train deep learning models, which are shown to rival the physics-based predictors. These neural networks managed to infer the electrostatic contributions of different chemical groups and learned the importance of solvent exposure and close interactions, including hydrogen bonds. Although trained only using theoretical data, our pKAI+ model displayed the best accuracy in a test set of ∼750 experimental values. Inference times allow speedups of more than 1000× compared to physics-based methods. By combining speed, accuracy, and a reasonable understanding of the underlying physics, our models provide a game-changing solution for fast estimations of macroscopic pKa values from ensembles of microscopic values as well as for many downstream applications such as molecular docking and constant-pH molecular dynamics simulations.
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Affiliation(s)
| | - Marco Bertolini
- Machine Learning Research, Bayer A.G., Berlin 13353, Germany
| | | | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via Melen 83, B Block, Genoa 16152, Italy
| | - Miguel Machuqueiro
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Campo Grande, Lisboa 1749-016, Portugal
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29
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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30
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Cons BD, Twigg DG, Kumar R, Chessari G. Electrostatic Complementarity in Structure-Based Drug Design. J Med Chem 2022; 65:7476-7488. [PMID: 35512344 DOI: 10.1021/acs.jmedchem.2c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimization of electrostatic complementarity is an important strategy in structure-based drug discovery for improving the affinity of molecules against a specific protein target. In this Miniperspective we identify examples where deliberate optimization of protein-ligand electrostatic complementarity or intramolecular electrostatic interactions gave improvements in target affinity (up to 250-fold), physicochemical properties, in vitro properties, and off-target selectivity. We also look retrospectively at a series of factor Xa inhibitors that show an almost 8000-fold range in potency that can be correlated with the calculated electrostatic potential (ESP) surfaces. Recent developments using a graph-convolutional deep neural network to rapidly generate high quality ESP surfaces have the potential to make this useful tool more accessible for a wider audience within the field of medicinal chemistry.
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Affiliation(s)
- Benjamin D Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Rajendra Kumar
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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31
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Chen AY, Lee J, Damjanovic A, Brooks BR. Protein p Ka Prediction by Tree-Based Machine Learning. J Chem Theory Comput 2022; 18:2673-2686. [PMID: 35289611 PMCID: PMC10510853 DOI: 10.1021/acs.jctc.1c01257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protonation states of ionizable protein residues modulate many essential biological processes. For correct modeling and understanding of these processes, it is crucial to accurately determine their pKa values. Here, we present four tree-based machine learning models for protein pKa prediction. The four models, Random Forest, Extra Trees, eXtreme Gradient Boosting (XGBoost), and Light Gradient Boosting Machine (LightGBM), were trained on three experimental PDB and pKa datasets, two of which included a notable portion of internal residues. We observed similar performance among the four machine learning algorithms. The best model trained on the largest dataset performs 37% better than the widely used empirical pKa prediction tool PROPKA and 15% better than the published result from the pKa prediction method DelPhiPKa. The overall root-mean-square error (RMSE) for this model is 0.69, with surface and buried RMSE values being 0.56 and 0.78, respectively, considering six residue types (Asp, Glu, His, Lys, Cys, and Tyr), and 0.63 when considering Asp, Glu, His, and Lys only. We provide pKa predictions for proteins in human proteome from the AlphaFold Protein Structure Database and observed that 1% of Asp/Glu/Lys residues have highly shifted pKa values close to the physiological pH.
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Affiliation(s)
- Ada Y. Chen
- Department of Physics & Astronomy, Johns Hopkins
University, Baltimore, Maryland, 21218
- Laboratory of Computational Biology, National Heart, Lung
and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Juyong Lee
- Department of Chemistry, Division of Chemistry and
Biochemistry, Kangwon National University, 1 Gangwondaehak-gil, Chuncheon, 24341,
Republic of Korea
| | - Ana Damjanovic
- Department of Biophysics, Johns Hopkins University,
Baltimore, Maryland, 21218
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung
and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
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32
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Khaniya U, Mao J, Wei RJ, Gunner MR. Characterizing Protein Protonation Microstates Using Monte Carlo Sampling. J Phys Chem B 2022; 126:2476-2485. [PMID: 35344367 PMCID: PMC8997239 DOI: 10.1021/acs.jpcb.2c00139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The ΔG, ΔH, and ΔS between the four protonation states of Glu35 and Asp52 in lysozyme are shown to be calculated with reasonable precision. At pH 7 the lysozyme charge ranges from 6 to 10, with 24 accepted protonation microstates, while RCs have ≈50,000. A weighted Pearson correlation analysis shows coupling between residue protonation states in RCs and how they change when the quinone in the QB site is reduced. Protonation microstates can be used to define input MD parameters and provide insight into the motion of protons coupled to reactions.
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Affiliation(s)
- Umesh Khaniya
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - Junjun Mao
- Department of Physics, City College of New York, New York, New York 10031, United States
| | - Rongmei Judy Wei
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - M R Gunner
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, The Graduate Center, City University of New York, New York, New York 10016, United States.,Department of Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
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33
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Ali F, Shafaa MW, Amin M. Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I. BIOLOGY 2022; 11:biology11030362. [PMID: 35336736 PMCID: PMC8945787 DOI: 10.3390/biology11030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
Abstract
Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron-sulfur cluster FX, which is followed by two terminal iron-sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint Em potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.
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Affiliation(s)
- Fedaa Ali
- Medical Biophysics Division, Department of Physics, Faculty of Science, Helwan University, Cairo 11795, Egypt; (F.A.); (M.W.S.)
- Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Medhat W. Shafaa
- Medical Biophysics Division, Department of Physics, Faculty of Science, Helwan University, Cairo 11795, Egypt; (F.A.); (M.W.S.)
| | - Muhamed Amin
- Department of Sciences, University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
- Universiteit Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9718 BG Groningen, The Netherlands
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Correspondence:
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34
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Gokcan H, Isayev O. Prediction of protein p K a with representation learning. Chem Sci 2022; 13:2462-2474. [PMID: 35310485 PMCID: PMC8864681 DOI: 10.1039/d1sc05610g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/29/2022] [Indexed: 11/21/2022] Open
Abstract
The behavior of proteins is closely related to the protonation states of the residues. Therefore, prediction and measurement of pK a are essential to understand the basic functions of proteins. In this work, we develop a new empirical scheme for protein pK a prediction that is based on deep representation learning. It combines machine learning with atomic environment vector (AEV) and learned quantum mechanical representation from ANI-2x neural network potential (J. Chem. Theory Comput. 2020, 16, 4192). The scheme requires only the coordinate information of a protein as the input and separately estimates the pK a for all five titratable amino acid types. The accuracy of the approach was analyzed with both cross-validation and an external test set of proteins. Obtained results were compared with the widely used empirical approach PROPKA. The new empirical model provides accuracy with MAEs below 0.5 for all amino acid types. It surpasses the accuracy of PROPKA and performs significantly better than the null model. Our model is also sensitive to the local conformational changes and molecular interactions.
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Affiliation(s)
- Hatice Gokcan
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA USA
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA USA
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35
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Jambrec D, Gebala M. DNA Electrostatics: From Theory to Application. ChemElectroChem 2022. [DOI: 10.1002/celc.202101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytische Chemie – Elektroanalytik & Sensorik Ruhr-Universität Bochum Universitätsstr. 150 D-44780 Bochum Germany
| | - Magdalena Gebala
- Department of Biochemistry Stanford University Stanford 94305, CA USA
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36
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Mazzei L, Musiani F, Żerko S, Koźminski W, Cianci M, Beniamino Y, Ciurli S, Zambelli B. Structure, dynamics, and function of SrnR, a transcription factor for nickel-dependent gene expression. Metallomics 2021; 13:6445039. [PMID: 34850061 DOI: 10.1093/mtomcs/mfab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/18/2021] [Indexed: 11/14/2022]
Abstract
Streptomyces griseus, a bacterium producing antibacterial drugs and featuring possible application in phytoremediation, expresses two metal-dependent superoxide dismutase (SOD) enzymes, containing either Fe(II) or Ni(II) in their active site. In particular, the alternative expression of the two proteins occurs in a metal-dependent mode, with the Fe(II)-enzyme gene (sodF) repressed at high intracellular Ni(II) concentrations by a two-component system (TCS). This complex involves two proteins, namely SgSrnR and SgSrnQ, which represent the transcriptional regulator and the Ni(II) sensor of the system, respectively. SgSrnR belongs to the ArsR/SmtB family of metal-dependent transcription factors; in the apo-form and in the absence of SgSrnQ, it can bind the DNA operator of sodF, upregulating gene transcription. According to a recently proposed hypothesis, Ni(II) binding to SgSrnQ would promote its interaction with SgSrnR, causing the release of the complex from DNA and the consequent downregulation of the sodF expression. SgSrnQ is predicted to be highly disordered, thus the understanding, at the molecular level, of how the SgSrnR/SgSrnQ TCS specifically responds to Ni(II) requires the knowledge of the structural, dynamic, and functional features of SgSrnR. These were investigated synergistically in this work using X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, atomistic molecular dynamics calculations, isothermal titration calorimetry, and in silico molecular docking. The results reveal that the homodimeric apo-SgSrnR binds to its operator in a two-step process that involves the more rigid globular portion of the protein and leaves its largely disordered regions available to possibly interact with the disordered SgSrnQ in a Ni-dependent process.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna. Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna. Italy
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźminski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, I-60131 Ancona, Italy
| | - Ylenia Beniamino
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna. Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna. Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna. Italy
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37
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Tam J, Palumbo T, Miwa JM, Chen BY. DiffBond: A Method for Predicting Intermolecular Bond Formation. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2021; 2021:2574-2586. [PMID: 35378834 DOI: 10.1109/bibm52615.2021.9669850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Many tools that explore models of protein complexes are also able to analyze interactions between specific residues and atoms. A comprehensive exploration of these interactions can often uncover aspects of protein-protein recognition that are not obvious using other protein analysis techniques. This paper describes DiffBond, a novel method for searching for intermolecular interactions between protein complexes while differentiating between three different types of interaction: hydrogen bonds, ionic bonds, and salt bridges. DiffBond incorporates textbook definitions of these three interactions while contending with uncertainties that are inherent in computational models of interacting proteins. We used it to examine the barnase-barstar, Rap1a-raf, and Smad2-Smad4 complexes, as well as a subset of protein complexes formed between three-finger toxins and nAChRs. Based on electrostatic interactions established by previous experimental studies, DiffBond was able to identify ionic and hydrogen bonds with high precision and recall, and identify salt bridges with high precision. In combination with other electrostatic analysis methods, DiffBond can be a useful tool in helping predict influential amino acids in protein-protein interactions and characterizing the type of interaction.
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Affiliation(s)
- Justin Tam
- Dept. Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Talulla Palumbo
- Dept. Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Julie M Miwa
- Dept. Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Brian Y Chen
- Dept. Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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38
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Kucherova A, Strango S, Sukenik S, Theillard M. Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike. JOURNAL OF COMPUTATIONAL PHYSICS 2021; 444:110591. [PMID: 36532662 PMCID: PMC9749448 DOI: 10.1016/j.jcp.2021.110591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We present a new approach to compute and analyze the dynamical electro-geometric properties of proteins undergoing conformational changes. The molecular trajectory is obtained from Markov state models, and the electrostatic potential is calculated using the continuum Poisson-Boltzmann equation. The numerical electric potential is constructed using a parallel sharp numerical solver implemented on adaptive Octree grids. We introduce novel a posteriori error estimates to quantify the solution's accuracy on the molecular surface. To illustrate the approach, we consider the opening of the SARS-CoV-2 spike protein using the recent molecular trajectory simulated through the Folding@home initiative. We analyze our results, focusing on the characteristics of the receptor-binding domain and its vicinity. This work lays the foundation for a new class of hybrid computational approaches, producing high-fidelity dynamical computational measurements serving as a basis for protein bio-mechanism investigations.
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Affiliation(s)
- Anna Kucherova
- Department of Applied Mathematics, University of California, Merced, CA 95343, USA
| | - Selma Strango
- Department of Applied Mathematics, University of California, Merced, CA 95343, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA
| | - Maxime Theillard
- Department of Applied Mathematics, University of California, Merced, CA 95343, USA
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39
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Guo Y, Nishida N, Hoshino T. Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization. J Chem Inf Model 2021; 61:4571-4581. [PMID: 34565151 DOI: 10.1021/acs.jcim.1c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.
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Affiliation(s)
- Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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40
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Siryk SV, Bendandi A, Diaspro A, Rocchia W. Charged dielectric spheres interacting in electrolytic solution: A linearized Poisson-Boltzmann equation model. J Chem Phys 2021; 155:114114. [PMID: 34551534 DOI: 10.1063/5.0056120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present an analytical theory of electrostatic interactions of two spherical dielectric particles of arbitrary radii and dielectric constants, immersed into a polarizable ionic solvent (assuming that the linearized Poisson-Boltzmann framework holds) and bearing arbitrary charge distributions expanded in multipolar terms. The presented development entails a novel two-center re-expansion analytical theory that expands upon and improves the existing ones, bypassing the conventional expansions in modified Bessel functions. On this basis, we develop a specific matrix formalism that facilitates the construction of asymptotic expansions in ascending order of Debye screening terms of potential coefficients, which are then employed to find exact closed-form expressions for the total electrostatic energy. In particular, this work allows us to explicitly and precisely quantify the k-screened terms of the potential coefficients and mutual interaction energy. Specific cases of monopolar and dipolar distributions are described in particular detail. Comprehensive numerical examples and tests of series convergence and the relative balance of leading and higher-order terms of the mutual interaction energy are presented depending on the inter-particle distance and particles' radii. The results of this work find application in soft matter modeling and, in particular, in computational biophysics and colloid science, where the availability of increasingly larger experimental structures at the atomic-level resolution makes numerical treatment challenging and calls for more efficient expressions and an increased range of validity.
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Affiliation(s)
- Sergii V Siryk
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
| | - Artemi Bendandi
- CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
| | - Alberto Diaspro
- CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
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41
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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42
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pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations. Methods Mol Biol 2021. [PMID: 34302677 DOI: 10.1007/978-1-0716-1468-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The conformational changes of membrane proteins are crucial to their function and usually lead to fluctuations in the electrostatic environment of the protein surface. A very effective way to quantify these changes is by calculating the pK a values of the protein's titratable residues, which can be regarded as electrostatic probes. To achieve this, we need to take advantage of the fast and reliable pK a calculators developed for globular proteins and adapt them to include the explicit effects of membranes. Here, we provide a detailed linear response approximation protocol that uses our own software (PypKa) to calculate reliable pK a values from short MD simulations of membrane proteins.
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43
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Corbella M, Liao Q, Moreira C, Parracino A, Kasson PM, Kamerlin SCL. The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition. J Phys Chem B 2021; 125:6791-6806. [PMID: 34137249 PMCID: PMC8279559 DOI: 10.1021/acs.jpcb.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA-binding proteins
play an important role in gene regulation
and cellular function. The transcription factors MarA and Rob are
two homologous members of the AraC/XylS family that regulate multidrug
resistance. They share a common DNA-binding domain, and Rob possesses
an additional C-terminal domain that permits binding of low-molecular
weight effectors. Both proteins possess two helix-turn-helix (HTH)
motifs capable of binding DNA; however, while MarA interacts with
its promoter through both HTH-motifs, prior studies indicate that
Rob binding to DNA via a single HTH-motif is sufficient for tight
binding. In the present work, we perform microsecond time scale all-atom
simulations of the binding of both transcription factors to different
DNA sequences to understand the determinants of DNA recognition and
binding. Our simulations characterize sequence-dependent changes in
dynamical behavior upon DNA binding, showcasing the role of Arg40
of the N-terminal HTH-motif in allowing for specific tight binding.
Finally, our simulations demonstrate that an acidic C-terminal loop
of Rob can control the DNA binding mode, facilitating interconversion
between the distinct DNA binding modes observed in MarA and Rob. In
doing so, we provide detailed molecular insight into DNA binding and
recognition by these proteins, which in turn is an important step
toward the efficient design of antivirulence agents that target these
proteins.
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Affiliation(s)
- Marina Corbella
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Cátia Moreira
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Antonietta Parracino
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-65124, Sweden.,Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, United States
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44
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Sequeiros-Borja CE, Surpeta B, Brezovsky J. Recent advances in user-friendly computational tools to engineer protein function. Brief Bioinform 2021; 22:bbaa150. [PMID: 32743637 PMCID: PMC8138880 DOI: 10.1093/bib/bbaa150] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein-protein and protein-nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.
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Affiliation(s)
- Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw
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Zhang Y, He X, Zhai J, Ji B, Man VH, Wang J. In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Brief Bioinform 2021; 22:6278153. [PMID: 34013346 PMCID: PMC8194596 DOI: 10.1093/bib/bbab188] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/30/2021] [Accepted: 04/22/2021] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel coronavirus, has brought an unprecedented pandemic to the world and affected over 64 million people. The virus infects human using its spike glycoprotein mediated by a crucial area, receptor-binding domain (RBD), to bind to the human ACE2 (hACE2) receptor. Mutations on RBD have been observed in different countries and classified into nine types: A435S, D364Y, G476S, N354D/D364Y, R408I, V341I, V367F, V483A and W436R. Employing molecular dynamics (MD) simulation, we investigated dynamics and structures of the complexes of the prototype and mutant types of SARS-CoV-2 spike RBDs and hACE2. We then probed binding free energies of the prototype and mutant types of RBD with hACE2 protein by using an end-point molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. According to the result of MM-PBSA binding free energy calculations, we found that V367F and N354D/D364Y mutant types showed enhanced binding affinities with hACE2 compared to the prototype. Our computational protocols were validated by the successful prediction of relative binding free energies between prototype and three mutants: N354D/D364Y, V367F and W436R. Thus, this study provides a reliable computational protocol to fast assess the existing and emerging RBD mutations. More importantly, the binding hotspots identified by using the molecular mechanics generalized Born surface area (MM-GBSA) free energy decomposition approach can guide the rational design of small molecule drugs or vaccines free of drug resistance, to interfere with or eradicate spike-hACE2 binding.
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Affiliation(s)
- Yuzhao Zhang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jingchen Zhai
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Beihong Ji
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
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46
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Cetin A. In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors. Chem Phys Lett 2021; 771:138563. [PMID: 33776065 PMCID: PMC7983322 DOI: 10.1016/j.cplett.2021.138563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
COVID-19, a new strain of coronavirus family, was identified at the end of 2019 in China. The COVID-19 virus spread rapidly all over the world. Scientists strive to find virus-specific antivirals for the treatment of COVID-19. The present study reports a molecular docking study of the stilbenolignans and SARS-CoV-2 main protease (SARS-CoV-2 Mpro) inhibitors. The detailed interactions between the stilbenolignan analogues and SARS-CoV-2 Mpro inhibitors were determined as hydrophobic bonds, hydrogen bonds and electronic bonds, inhibition activity, ligand efficiency, bonding type and distance and etc. The binding energies of the stilbenolignan analogues were obtained from the molecular docking of SARS-CoV-2 Mpro. Lehmbachol D, Maackolin, Gnetucleistol, Gnetifolin F, Gnetofuran A and Aiphanol were found to be -7.7, -8.2, -7.3, -8.5, -8.0 and -7.3 kcal/mol, respectively. Osirus, Molinspiration and SwissADME chemoinformatic tools were used to examine ADMET properties, pharmacokinetic parameters and toxicological characteristics of the stilbenolignan analogues. All analogues obey the Lipinski's rule of five. Furthermore, stilbenolignan analogues were studied to predict their binding affinities against SARS-CoV-2 Mpro using molecular modeling and simulation techniques, and the binding free energy calculations of all complexes were calculated using the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) method. With the data presented here it has been observed that these analogues may be a good candidate for SARS-CoV-2 Mpro in vivo studies, so more research can be done on stilbenolignan analogues.
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Abstract
The dielectric response of a polar solvent to an ion is analyzed in terms of the bound charge, the net charge that accumulates near the ion as a consequence of the inhomogeneous polarization of the surrounding solvent. We demonstrate that the total bound charge arising in a full molecular treatment is identical to the total bound charge from standard continuum theory. In continuum theory, the bound charge resides in an infinitely thin layer, while in a molecular description the bound charge is spread over a region of finite width. Near simple atomic ions, the width of the bound charge distribution is roughly 1.3 nm. By simulating a sequence of ion charges from 0.1 to 2 e, where e is the magnitude of the electron charge, we analyze the applicability of linear response theory, which has been used by several authors. With increasing charge, the nonlinear response extends to an increasing distance from the ion. However, outside the region containing bound charge, the response is linear and in accord with continuum theory. Previous attempts to assign a dielectric constant to a solvent in the interfacial region are analyzed.
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Affiliation(s)
- Min-Sang Lee
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Sherwin J Singer
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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Lopez-Hernandez AE, Xie Y, Guo W, Li L. The Electrostatic Features of Dengue Virus Capsid Assembly. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dengue virus causes serious diseases and deaths in the world. Understanding the fundamental mechanisms of dengue virus is highly demanded to develop treatments for dengue virus caused diseases. Here, we present a computational work which focused on the stability of dengue viral capsid. The interactions among E proteins on the dengue viral capsid were studied using several computational approaches. It was found that the electrostatic distribution on a single E protein monomer is highly inhomogeneous, which makes an E protein strongly binding with another E protein. This is the reason why all the E proteins form homodimers as the basic units on the whole dengue viral capsids. The pKa calculations of E proteins demonstrated that the folding energy of an E protein is low and stable in the range of pH 6–10, which is different from many other proteins that are stable at certain pH. The pH dependence of binding energy of E protein homodimer shows that the binding energy is low and independent from pH when the pH is also in the range of 6–10. This finding implies that the dengue virus can survive in a wide range of pH, which can explain why the dengue virus is so widely distributed in the world and spreads fast.
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Affiliation(s)
| | - Yixin Xie
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
| | - Wenhan Guo
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
- Department of Physics, University of Texas at El Paso, El Paso, TX, USA
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Wang S, Alexov E, Zhao S. On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:1370-1405. [PMID: 33757190 PMCID: PMC9871984 DOI: 10.3934/mbe.2021072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Numerical treatment of singular charges is a grand challenge in solving the Poisson-Boltzmann (PB) equation for analyzing electrostatic interactions between the solute biomolecules and the surrounding solvent with ions. For diffuse interface PB models in which solute and solvent are separated by a smooth boundary, no effective algorithm for singular charges has been developed, because the fundamental solution with a space dependent dielectric function is intractable. In this work, a novel regularization formulation is proposed to capture the singularity analytically, which is the first of its kind for diffuse interface PB models. The success lies in a dual decomposition - besides decomposing the potential into Coulomb and reaction field components, the dielectric function is also split into a constant base plus space changing part. Using the constant dielectric base, the Coulomb potential is represented analytically via Green's functions. After removing the singularity, the reaction field potential satisfies a regularized PB equation with a smooth source. To validate the proposed regularization, a Gaussian convolution surface (GCS) is also introduced, which efficiently generates a diffuse interface for three-dimensional realistic biomolecules. The performance of the proposed regularization is examined by considering both analytical and GCS diffuse interfaces, and compared with the trilinear method. Moreover, the proposed GCS-regularization algorithm is validated by calculating electrostatic free energies for a set of proteins and by estimating salt affinities for seven protein complexes. The results are consistent with experimental data and estimates of sharp interface PB models.
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Affiliation(s)
- Siwen Wang
- Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487,USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Shan Zhao
- Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487,USA
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Wu X, Guo Q, Li Q, Wan S, Li Z, Zhang J. Molecular mechanism study of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 2021; 40:5848-5857. [PMID: 33459177 DOI: 10.1080/07391102.2021.1874530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ABTRACTThe epidermal growth factor receptor (EGFR) kinase inhibitors Gefitinib, Erlotinib, Afatinib and Osimertinib have been approved for the treatments of non-small cell lung cancer patients harboring sensitive EGFR mutations, but resistance arises rapidly. To date all approved EGFR inhibitors are ATP-competitive inhibitors, highlighting the need for therapeutic agents with alternative mechanisms of action. Allosteric kinase inhibitors offer a promising new therapeutic strategy to ATP-competitive inhibitors. The mutant-selective allosteric EGFR inhibitors EAI045 exhibited higher potency for EGFRL858R&T790M compared to WT, which was also effective in EGFR-mutant models including those harboring the C797S mutation. However, it was not effective as a single-agent inhibitor, and require the co-administration of the anti-EGFR antibody Cetuximab. Further efforts produced a more potent analog JBJ-04-125-02, which can inhibit cell proliferation as a single-agent inhibitor. In the present study, molecular dynamics simulations and free energy calculations were performed and revealed the detailed inhibitory mechanism of JBJ-04-125-02 as more potent EGFR inhibitor. Moreover, the energy difference between HOMO and LUMO calculated by DFT implied the higher interaction of JBJ-04-125-02 than EAI045 in the active site of the EGFR. The identified key features obtained from the molecular modeling enabled us to design novel EGFR allosteric inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaoyun Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, PR China
| | - Qian Guo
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, PR China
| | - Qinlan Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, PR China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, PR China
| | - Zhonghuang Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, PR China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, PR China
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