1
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Yu Y, Tian W, Grauffel C, Lin W, Hsieh M, Wu P, Lee H, Peng C, Lin P, Chu H, Lim C, Chang TW. An Antibody-Drug Conjugate for Multiple Myeloma Prepared by Multi-Arm Linkers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307852. [PMID: 38477561 PMCID: PMC11132082 DOI: 10.1002/advs.202307852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/31/2024] [Indexed: 03/14/2024]
Abstract
First-line treatment of multiple myeloma, a prevalent blood cancer lacking a cure, using anti-CD38 daratumumab antibody and lenalidomide is often inadequate due to relapse and severe side effects. To enhance drug safety and efficacy, an antibody-drug conjugate, TE-1146, comprising six lenalidomide drug molecules site-specifically conjugated to a reconfigured daratumumab to deliver cytotoxic lenalidomide to tumor cells is developed. TE-1146 is prepared using the HighDAR platform, which employs i) a maleimide-containing "multi-arm linker" to conjugate multiple drug molecules creating a drug bundle, and ii) a designed peptide with a Zn2+-binding cysteine at the C-termini of a reconfigured daratumumab for site-specific drug bundle conjugation. It is shown that TE-1146 remains intact and effectively enters CD38-expressing tumor cells, releasing lenalidomide, leading to enhanced cell-killing effects compared to lenalidomide/daratumumab alone or their combination. This reveals the remarkable potency of lenalidomide once internalized by myeloma cells. TE-1146 precisely delivers lenalidomide to target CD38-overexpressing tumor cells. In contrast, lenalidomide without daratumumab cannot easily enter cells, whereas daratumumab without lenalidomide relies on Fc-dependent effector functions to kill tumor cells.
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Affiliation(s)
- Yueh‐Hsiang Yu
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Wei‐Ting Tian
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | | | - Wei‐Chen Lin
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Ming‐Yu Hsieh
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Pei‐Wen Wu
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Hui‐Ju Lee
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Chi‐Jiun Peng
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Pei‐Hsuan Lin
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Hsing‐Mao Chu
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
| | - Carmay Lim
- Institute of Biomedical SciencesAcademia SinicaAcademia Rd.Taipei115Taiwan
| | - Tse Wen Chang
- Immunwork, Inc.Academia Rd., Sec. 1, NangangTaipei115Taiwan
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2
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Oszajca M, Drabik G, Radoń M, Franke A, van Eldik R, Stochel G. Experimental and Computational Insight into the Mechanism of NO Binding to Ferric Microperoxidase. The Likely Role of Tautomerization to Account for the pH Dependence. Inorg Chem 2021; 60:15948-15967. [PMID: 34476946 DOI: 10.1021/acs.inorgchem.1c00933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
According to the current paradigm, the metal-hydroxo bond in a six-coordinate porphyrin complex is believed to be significantly less reactive in ligand substitution than the analogous metal-aqua bond, due to a much higher strength of the former bond. Here, we report kinetic studies for nitric oxide (NO) binding to a heme-protein model, acetylated microperoxidase-11 (AcMP-11), that challenge this paradigm. In the studied pH range 7.4-12.6, ferric AcMP-11 exists in three acid-base forms, assigned in the literature as [(AcMP-11)FeIII(H2O)(HisH)] (1), [(AcMP-11)FeIII(OH)(HisH)] (2), and [(AcMP-11)FeIII(OH)(His-)] (3). From the pH dependence of the second-order rate constant for NO binding (kon), we determined individual rate constants characterizing forms 1-3, revealing only a ca. 10-fold decrease in the NO binding rate on going from 1 (kon(1) = 3.8 × 106 M-1 s-1) to 2 (kon(2) = 4.0 × 105 M-1 s-1) and the inertness of 3. These findings lead to the abandonment of the dissociatively activated mechanism, in which the reaction rate can be directly correlated with the Fe-OH bond energy, as the mechanistic explanation for the process with regard to 2. The reactivity of 2 is accounted for through the existence of a tautomeric equilibrium between the major [(AcMP-11)FeIII(OH)(HisH)] (2a) and minor [(AcMP-11)FeIII(H2O)(His-)] (2b) species, of which the second one is assigned as the NO binding target due to its labile Fe-OH2 bond. The proposed mechanism is further substantiated by quantum-chemical calculations, which confirmed both the significant labilization of the Fe-OH2 bond in the [(AcMP-11)FeIII(H2O)(His-)] tautomer and the feasibility of the tautomer formation, especially after introducing empirical corrections to the computed relative acidities of the H2O and HisH ligands based on the experimental pKa values. It is shown that the "effective lability" of the axial ligand (OH-/H2O) in 2 may be comparable to the lability of the H2O ligand in 1.
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Affiliation(s)
- Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Gabriela Drabik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alicja Franke
- Department of Chemistry, Ludwigs-Maximilians University, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Rudi van Eldik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.,Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstr. 1, 91058 Erlangen, Germany.,Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Grażyna Stochel
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
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3
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Xu M, Zhu T, Zhang JZH. Automatically Constructed Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins. Front Chem 2021; 9:692200. [PMID: 34222200 PMCID: PMC8249736 DOI: 10.3389/fchem.2021.692200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The development of accurate and efficient potential energy functions for the molecular dynamics simulation of metalloproteins has long been a great challenge for the theoretical chemistry community. An artificial neural network provides the possibility to develop potential energy functions with both the efficiency of the classical force fields and the accuracy of the quantum chemical methods. In this work, neural network potentials were automatically constructed by using the ESOINN-DP method for typical zinc proteins. For the four most common zinc coordination modes in proteins, the potential energy, atomic forces, and atomic charges predicted by neural network models show great agreement with quantum mechanics calculations and the neural network potential can maintain the coordination geometry correctly. In addition, MD simulation and energy optimization with the neural network potential can be readily used for structural refinement. The neural network potential is not limited by the function form and complex parameterization process, and important quantum effects such as polarization and charge transfer can be accurately considered. The algorithm proposed in this work can also be directly applied to proteins containing other metal ions.
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Affiliation(s)
- Mingyuan Xu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
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4
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Grauffel C, Dudev T, Lim C. Metal Affinity/Selectivity of Monophosphate-Containing Signaling/Lipid Molecules. J Chem Theory Comput 2021; 17:2444-2456. [PMID: 33818070 DOI: 10.1021/acs.jctc.0c01007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monophosphate, an essential component of nucleic acids, as well as cell membranes and signaling molecules, is often bound to metal cations. Despite the biological importance of monophosphate-containing cell-signaling or lipid molecules, their propensity to bind the two most abundant cellular dications, Mg2+ and Ca2+, in a particular mode (inner/outer shell, mono/bidentate) is not well understood. Whether they prefer binding to Mg2+ than to Ca2+ and if they can outcompete the carboxylates of excitatory Asp/Glu and inhibitory gamma-aminobutyric acid (GABA) neurotransmitters in binding to Mg2+/Ca2+ remain unclear. To address these questions, we modeled cyclic adenosine/guanosine monophosphate (cAMP/cGMP), nucleoside 2',3'-cyclic phosphate, phosphatidylinositol (PI), phosphatidylserine (PS), and phosphatidylethanolamine (PEA) and determined their most stable metal-binding modes, including those of Asp/Glu and GABA, as well as their selectivity for Mg2+/Ca2+ using density functional theory combined with the polarizable continuum model. The results obtained, which are consistent with the available experimental findings, reveal that the structurally and functionally diverse monophosphate-containing ligands studied prefer monodentate coordination of Mg2+ because of the greater strain encountered upon bidentate coordination, whereas the larger Ca2+ imposes less strain upon bidentate binding and has reduced/no preference for monodentate coordination. We further show that in a low-dielectric environment, negatively charged monophosphate-containing ligands favor the better charge-accepting dication, that is, Mg2+ rather than Ca2+. By promoting Mg2+ over Ca2+ binding, signaling monophosphates (cAMP/cGMP) do not entrap cellular Ca2+ and interfere with signal transduction processes employing Ca2+ as a second messenger. In regions with high glutamate cytoplasmic concentration, glutamate may sequester Mg2+ bound to isolated five-/six-membered ring phosphates, PI, or neutral PEA, but not anionic phospholipids constituting the inner leaflet of the cell membrane.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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5
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Silverstein TP. How enzymes harness highly unfavorable proton transfer reactions. Protein Sci 2021; 30:735-744. [PMID: 33554401 DOI: 10.1002/pro.4037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/12/2022]
Abstract
Acid-base reactions that are exceedingly unfavorable under standard conditions can be catalytically important at enzyme active sites. For example, in triose phosphate isomerase, a glutamate side chain (nominal pKa ≈ 4 in solution) can in fact deprotonate a CH group that is vicinal to a carbonyl (pKa ≈ 18 in solution). This is true because of three distinct interactions: (a) ground state pKa shifts due to environment polarity and electrostatics; (b) dramatic increases in effective molarity due to optimization of proximity and orientation; and (c) transition state pKa shifts due to binding interactions and the formation of strong low barrier hydrogen bonds. In this report, we review the literature showing that the sum of these three effects supplies more than enough free energy to push forward proton transfer reactions that under standard conditions are exceedingly nonspontaneous and slow.
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6
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Sinha V, Laan JJ, Pidko EA. Accurate and rapid prediction of pKa of transition metal complexes: semiempirical quantum chemistry with a data-augmented approach. Phys Chem Chem Phys 2021; 23:2557-2567. [DOI: 10.1039/d0cp05281g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Data-augmented high-throughput QM approach to compute pKa of transition metal hydride complexes with hDFT accuracy and low cost.
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Affiliation(s)
- Vivek Sinha
- Inorganic Systems Engineering
- Department of Chemical Engineering
- Faculty of Applied Sciences
- Delft University of Technology
- Delft
| | - Jochem J. Laan
- Inorganic Systems Engineering
- Department of Chemical Engineering
- Faculty of Applied Sciences
- Delft University of Technology
- Delft
| | - Evgeny A. Pidko
- Inorganic Systems Engineering
- Department of Chemical Engineering
- Faculty of Applied Sciences
- Delft University of Technology
- Delft
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7
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Mazmanian K, Sargsyan K, Lim C. How the Local Environment of Functional Sites Regulates Protein Function. J Am Chem Soc 2020; 142:9861-9871. [PMID: 32407086 DOI: 10.1021/jacs.0c02430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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8
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Lee YM, Grauffel C, Chen T, Sargsyan K, Lim C. Factors Governing the Different Functions of Zn2+-Sites with Identical Ligands in Proteins. J Chem Inf Model 2019; 59:3946-3954. [DOI: 10.1021/acs.jcim.9b00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Ting Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300 Taiwan
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9
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Grauffel C, Lim C. Factors governing when a metal-bound water is deprotonated in proteins. Phys Chem Chem Phys 2018; 20:29625-29636. [DOI: 10.1039/c8cp04776f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We evaluate the extent to which the pKw depends on the type, number, and metal-binding mode of the first-shell ligands, the metal–ligand bond distances, first-shell⋯second-shell H-bonding interactions, and the protein environment.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 115
- Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 115
- Taiwan
- Department of Chemistry
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