1
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Inan T, Flinko R, Lewis GK, MacKerell AD, Kurkcuoglu O. Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation. J Phys Chem B 2024; 128:5157-5174. [PMID: 38647430 PMCID: PMC11139592 DOI: 10.1021/acs.jpcb.4c00925] [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: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The chemokine receptor CXCR4 is a critical target for the treatment of several cancer types and HIV-1 infections. While orthosteric and allosteric modulators have been developed targeting its extracellular or transmembrane regions, the intramembrane region of CXCR4 may also include allosteric binding sites suitable for the development of allosteric drugs. To investigate this, we apply the Gaussian Network Model (GNM) to the monomeric and dimeric forms of CXCR4 to identify residues essential for its local and global motions located in the hinge regions of the protein. Residue interaction network (RIN) analysis suggests hub residues that participate in allosteric communication throughout the receptor. Mutual residues from the network models reside in regions with a high capacity to alter receptor dynamics upon ligand binding. We then investigate the druggability of these potential allosteric regions using the site identification by ligand competitive saturation (SILCS) approach, revealing two putative allosteric sites on the monomer and three on the homodimer. Two screening campaigns with Glide and SILCS-Monte Carlo docking using FDA-approved drugs suggest 20 putative hit compounds including antifungal drugs, anticancer agents, HIV protease inhibitors, and antimalarial drugs. In vitro assays considering mAB 12G5 and CXCL12 demonstrate both positive and negative allosteric activities of these compounds, supporting our computational approach. However, in vivo functional assays based on the recruitment of β-arrestin to CXCR4 do not show significant agonism and antagonism at a single compound concentration. The present computational pipeline brings a new perspective to computer-aided drug design by combining conformational dynamics based on network analysis and cosolvent analysis based on the SILCS technology to identify putative allosteric binding sites using CXCR4 as a showcase.
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Affiliation(s)
- Tugce Inan
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
| | - Robin Flinko
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - George K. Lewis
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- University
of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Maryland, Baltimore, Maryland 21201, United States
| | - Ozge Kurkcuoglu
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
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2
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Deng J, Cui Q. Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1897-1911. [PMID: 38417108 DOI: 10.1021/acs.jctc.4c00013] [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: 03/01/2024]
Abstract
Prediction of the hydration levels of protein cavities and active sites is important to both mechanistic analysis and ligand design. Due to the unique microscopic environment of these buried water molecules, a polarizable model is expected to be crucial for an accurate treatment of protein internal hydration in simulations. Here we adapt a nonequilibrium candidate Monte Carlo approach for conducting grand canonical Monte Carlo simulations with the Drude polarizable force field. The GPU implementation enables the efficient sampling of internal cavity hydration levels in biomolecular systems. We also develop an enhanced sampling approach referred to as B-walking, which satisfies detailed balance and readily combines with grand canonical integration to efficiently calculate quantitative binding free energies of water to protein cavities. Applications of these developments are illustrated in a solvent box and the polar ligand binding site in trypsin. Our simulation results show that including electronic polarization leads to a modest but clear improvement in the description of water position and occupancy compared to the crystal structure. The B-walking approach enhances the range of water sampling in different chemical potential windows and thus improves the accuracy of water binding free energy calculations.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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3
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Jiang W, Wijerathne TD, Zhang H, Lin YC, Jo S, Im W, Lacroix JJ, Luo YL. Structural and thermodynamic framework for PIEZO1 modulation by small molecules. Proc Natl Acad Sci U S A 2023; 120:e2310933120. [PMID: 38060566 PMCID: PMC10723123 DOI: 10.1073/pnas.2310933120] [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: 06/28/2023] [Accepted: 10/12/2023] [Indexed: 12/17/2023] Open
Abstract
Mechanosensitive PIEZO channels constitute potential pharmacological targets for multiple clinical conditions, spurring the search for potent chemical PIEZO modulators. Among them is Yoda1, a widely used synthetic small molecule PIEZO1 activator discovered through cell-based high-throughput screening. Yoda1 is thought to bind to PIEZO1's mechanosensory arm domain, sandwiched between two transmembrane regions near the channel pore. However, how the binding of Yoda1 to this region promotes channel activation remains elusive. Here, we first demonstrate that cross-linking PIEZO1 repeats A and B with disulfide bridges reduces the effects of Yoda1 in a redox-dependent manner, suggesting that Yoda1 acts by perturbing the contact between these repeats. Using molecular dynamics-based absolute binding free energy simulations, we next show that Yoda1 preferentially occupies a deeper, amphipathic binding site with higher affinity in PIEZO1 open state. Using Yoda1's binding poses in open and closed states, relative binding free energy simulations were conducted in the membrane environment, recapitulating structure-activity relationships of known Yoda1 analogs. Through virtual screening of an 8 million-compound library using computed fragment maps of the Yoda1 binding site, we subsequently identified two chemical scaffolds with agonist activity toward PIEZO1. This study supports a pharmacological model in which Yoda1 activates PIEZO1 by wedging repeats A and B, providing a structural and thermodynamic framework for the rational design of PIEZO1 modulators. Beyond PIEZO channels, the three orthogonal computational approaches employed here represent a promising path toward drug discovery in highly heterogeneous membrane protein systems.
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Affiliation(s)
- Wenjuan Jiang
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Tharaka D. Wijerathne
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Han Zhang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015
- Department of Chemistry, Lehigh University, Bethlehem, PA18015
- Department of Bioengineering, Lehigh University, Bethlehem, PA18015
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA18015
| | - Yi-Chun Lin
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Sunhwan Jo
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD21201
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015
- Department of Chemistry, Lehigh University, Bethlehem, PA18015
- Department of Bioengineering, Lehigh University, Bethlehem, PA18015
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA18015
| | - Jerome J. Lacroix
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Yun L. Luo
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
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4
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Pandey P, MacKerell AD. Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. J Chem Inf Model 2023; 63:5903-5915. [PMID: 37682640 PMCID: PMC10603762 DOI: 10.1021/acs.jcim.3c00514] [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] [Indexed: 09/10/2023]
Abstract
Membrane permeability of drug molecules plays a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based site identification by ligand competitive saturation (SILCS) method and data-driven artificial intelligence (AI) to create a high-throughput predictive model for the passive permeability of druglike molecules. In this study, we present a comparative analysis of four regression models to predict membrane permeabilities of small druglike molecules; of the tested models, Random Forest was the most predictive yielding an R2 of 0.81 for the independent data set. The input feature vector used to train the developed prediction model includes absolute free energy profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. The use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability, while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design.
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Affiliation(s)
- Poonam Pandey
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
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5
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Olson KM, Devereaux AL, Chatterjee P, Saldaña-Shumaker SL, Shafer A, Plotkin A, Kandasamy R, MacKerell AD, Traynor JR, Cunningham CW. Nitro-benzylideneoxymorphone, a bifunctional mu and delta opioid receptor ligand with high mu opioid receptor efficacy. Front Pharmacol 2023; 14:1230053. [PMID: 37469877 PMCID: PMC10352325 DOI: 10.3389/fphar.2023.1230053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction: There is a major societal need for analgesics with less tolerance, dependence, and abuse liability. Preclinical rodent studies suggest that bifunctional ligands with both mu (MOPr) and delta (DOPr) opioid peptide receptor activity may produce analgesia with reduced tolerance and other side effects. This study explores the structure-activity relationships (SAR) of our previously reported MOPr/DOPr lead, benzylideneoxymorphone (BOM) with C7-methylene-substituted analogs. Methods: Analogs were synthesized and tested in vitro for opioid receptor binding and efficacy. One compound, nitro-BOM (NBOM, 12) was evaluated for antinociceptive effects in the warm water tail withdrawal assay in C57BL/6 mice. Acute and chronic antinociception was determined, as was toxicologic effects on chronic administration. Molecular modeling experiments were performed using the Site Identification by Ligand Competitive Saturation (SILCS) method. Results: NBOM was found to be a potent MOPr agonist/DOPr partial agonist that produces high-efficacy antinociception. Antinociceptive tolerance was observed, as was weight loss; this toxicity was only observed with NBOM and not with BOM. Modeling supports the hypothesis that the increased MOPr efficacy of NBOM is due to the substituted benzylidene ring occupying a nonpolar region within the MOPr agonist state. Discussion: Though antinociceptive tolerance and non-specific toxicity was observed on repeated administration, NBOM provides an important new tool for understanding MOPr/DOPr pharmacology.
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Affiliation(s)
- Keith M. Olson
- Department of Pharmacology and Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Andrea L. Devereaux
- Department of Pharmaceutical Sciences, Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
| | - Payal Chatterjee
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Savanah L. Saldaña-Shumaker
- Department of Pharmaceutical Sciences, Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
| | - Amanda Shafer
- Department of Pharmacology and Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Adam Plotkin
- Department of Pharmaceutical Sciences, Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
| | - Ram Kandasamy
- Department of Pharmacology and Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States
- Department of Psychology, California State University, East Bay, Hayward, CA, United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - John R. Traynor
- Department of Pharmacology and Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Christopher W. Cunningham
- Department of Pharmaceutical Sciences, Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
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6
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Sengul MY, MacKerell AD. Influence of Mg 2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling. ACS OMEGA 2023; 8:19532-19546. [PMID: 37305323 PMCID: PMC10249389 DOI: 10.1021/acsomega.3c00931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/11/2023] [Indexed: 06/13/2023]
Abstract
Metal ions, particularly magnesium ions (Mg2+), play a role in stabilizing the tertiary structures of RNA molecules. Theoretical models and experimental techniques show that metal ions can change RNA dynamics and how it transitions through different stages of folding. However, the specific ways in which metal ions contribute to the formation and stabilization of RNA's tertiary structure are not fully understood at the atomic level. Here, we combined oscillating excess chemical potential Grand Canonical Monte Carlo (GCMC) and metadynamics to bias toward the sampling of unfolded states using reaction coordinates generated by machine learning allowing for examination of Mg2+-RNA interactions that contribute to stabilizing folded states of the pseudoknot found in the Twister ribozyme. GCMC is used to sample diverse ion distributions around the RNA with deep learning applied to iteratively generate system-specific reaction coordinates to maximize conformational sampling during metadynamics simulations. Results from 6 μs simulations performed on 9 individual systems indicate that Mg2+ ions play a crucial role in stabilizing the three-dimensional (3D) structure of the RNA by stabilizing specific interactions of phosphate groups or phosphate groups and bases of neighboring nucleotides. While many phosphates are accessible to interactions with Mg2+, it is observed that multiple, specific interactions are required to sample conformations close to the folded state; coordination of Mg2+ at individual specific sites facilitates sampling of folded conformations though unfolding ultimately occurs. It is only when multiple specific interactions occur, including the presence of specific inner-shell cation interactions linking two nucleotides, that conformations close to the folded state are stable. While many of the identified Mg2+ interactions are observed in the X-ray crystal structure of Twister, the present study suggests two new Mg2+ ion sites in the Twister ribozyme that contribute to stabilization. In addition, specific interactions with Mg2+ are observed that destabilize the local RNA structure, a process that may facilitate the folding of RNA into its correct structure.
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7
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Yu W, Weber DJ, MacKerell AD. Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation. J Chem Theory Comput 2023; 19:3007-3021. [PMID: 37115781 PMCID: PMC10205696 DOI: 10.1021/acs.jctc.3c00232] [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] [Indexed: 04/29/2023]
Abstract
Covalent drug design is an important component in drug discovery. Traditional drugs interact with their target in a reversible equilibrium, while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with targeted residues and thus may offer a more effective therapeutic approach. To facilitate the design of this class of ligands, computational methods can be used to help identify reactive nucleophilic residues, frequently cysteines, on a target protein for covalent binding, to test various warhead groups for their potential reactivities, and to predict noncovalent contributions to binding that can facilitate drug-target interactions that are important for binding specificity. To further aid covalent drug design, we extended a functional group mapping approach based on explicit solvent all-atom molecular simulations (SILCS: site identification by ligand competitive saturation) that intrinsically considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. Through docking of a library of representative warhead fragments using SILCS-Monte Carlo (SILCS-MC), reactive cysteines can be correctly identified for proteins being tested. Furthermore, a machine learning model was trained to quantify the effectiveness of various warhead groups for proteins using metrics from SILCS-MC as well as experimental model compound warhead reactivity data. The ability to rank covalent molecular binders with similar warheads using SILCS ligand grid free energy (LGFE) ranking was also tested for several proteins. Based on these tools, an integrated SILCS-based workflow was developed, named SILCS-Covalent, which can both qualitatively and quantitatively inform covalent drug discovery.
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Affiliation(s)
- Wenbo Yu
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - David J. Weber
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
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8
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Orr AA, Tao A, Guvench O, MacKerell AD. Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction. Mol Pharm 2023; 20:2600-2611. [PMID: 37017675 PMCID: PMC10159941 DOI: 10.1021/acs.molpharmaceut.3c00064] [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] [Indexed: 04/06/2023]
Abstract
Protein-based therapeutics typically require high concentrations of the active protein, which can lead to protein aggregation and high solution viscosity. Such solution behaviors can limit the stability, bioavailability, and manufacturability of protein-based therapeutics and are directly influenced by the charge of a protein. Protein charge is a system property affected by its environment, including the buffer composition, pH, and temperature. Thus, the charge calculated by summing the charges of each residue in a protein, as is commonly done in computational methods, may significantly differ from the effective charge of the protein as these calculations do not account for contributions from bound ions. Here, we present an extension of the structure-based approach termed site identification by ligand competitive saturation-biologics (SILCS-Biologics) to predict the effective charge of proteins. The SILCS-Biologics approach was applied on a range of protein targets in different salt environments for which membrane-confined electrophoresis-determined charges were previously reported. SILCS-Biologics maps the 3D distribution and predicted occupancy of ions, buffer molecules, and excipient molecules bound to the protein surface in a given salt environment. Using this information, the effective charge of the protein is predicted such that the concentrations of the ions and the presence of excipients or buffers are accounted for. Additionally, SILCS-Biologics also produces 3D structures of the binding sites of ions on the proteins, which enable further analyses such as the characterization of protein surface charge distribution and dipole moments in different environments. Notable is the capability of the method to account for competition between salts, excipients, and buffers on the calculated electrostatic properties in different protein formulations. Our study demonstrates the ability of the SILCS-Biologics approach to predict the effective charge of proteins and its applicability in uncovering protein-ion interactions and their contributions to protein solubility and function.
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Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Aoxiang Tao
- SilcsBio LLC, 1100 Wicomico Street, Suite 323, Baltimore, MD, USA
| | - Olgun Guvench
- SilcsBio LLC, 1100 Wicomico Street, Suite 323, Baltimore, MD, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
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9
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Zhao M, Kognole AA, Jo S, Tao A, Hazel A, MacKerell AD. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. J Comput Chem 2023. [PMID: 37093676 DOI: 10.1002/jcc.27121] [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: 11/14/2022] [Revised: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
The Grand Canonical Monte Carlo (GCMC) ensemble defined by the excess chemical potential, μex , volume, and temperature, in the context of molecular simulations allows for variations in the number of particles in the system. In practice, GCMC simulations have been widely applied for the sampling of rare gasses and water, but limited in the context of larger molecules. To overcome this limitation, the oscillating μex GCMC method was introduced and shown to be of utility for sampling small solutes, such as formamide, propane, and benzene, as well as for ionic species such as monocations, acetate, and methylammonium. However, the acceptance of GCMC insertions is low, and the method is computationally demanding. In the present study, we improved the sampling efficiency of the GCMC method using known cavity-bias and configurational-bias algorithms in the context of GPU architecture. Specifically, for GCMC simulations of aqueous solution systems, the configurational-bias algorithm was extended by applying system partitioning in conjunction with a random interval extraction algorithm, thereby improving the efficiency in a highly parallel computing environment. The method is parallelized on the GPU using CUDA and OpenCL, allowing for the code to run on both Nvidia and AMD GPUs, respectively. Notably, the method is particularly well suited for GPU computing as the large number of threads allows for simultaneous sampling of a large number of configurations during insertion attempts without additional computational overhead. In addition, the partitioning scheme allows for simultaneous insertion attempts for large systems, offering considerable efficiency. Calculations on the BK Channel, a transporter, including a lipid bilayer with over 760,000 atoms, show a speed up of ~53-fold through the use of system partitioning. The improved algorithm is then combined with an enhanced μex oscillation protocol and shown to be of utility in the context of the site-identification by ligand competitive saturation (SILCS) co-solvent sampling approach as illustrated through application to the protein CDK2.
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Affiliation(s)
- Mingtian Zhao
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | | | | | | | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
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10
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Karade SS, Franco EJ, Rojas AC, Hanrahan KC, Kolesnikov A, Yu W, MacKerell AD, Hill DC, Weber DJ, Brown AN, Treston AM, Mariuzza RA. Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum α-Glucosidase I with Anti-SARS-CoV-2 Activity. J Med Chem 2023; 66:2744-2760. [PMID: 36762932 PMCID: PMC10278443 DOI: 10.1021/acs.jmedchem.2c01750] [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] [Indexed: 02/11/2023]
Abstract
Enveloped viruses depend on the host endoplasmic reticulum (ER) quality control (QC) machinery for proper glycoprotein folding. The endoplasmic reticulum quality control (ERQC) enzyme α-glucosidase I (α-GluI) is an attractive target for developing broad-spectrum antivirals. We synthesized 28 inhibitors designed to interact with all four subsites of the α-GluI active site. These inhibitors are derivatives of the iminosugars 1-deoxynojirimycin (1-DNJ) and valiolamine. Crystal structures of ER α-GluI bound to 25 1-DNJ and three valiolamine derivatives revealed the basis for inhibitory potency. We established the structure-activity relationship (SAR) and used the Site Identification by Ligand Competitive Saturation (SILCS) method to develop a model for predicting α-GluI inhibition. We screened the compounds against SARS-CoV-2 in vitro to identify those with greater antiviral activity than the benchmark α-glucosidase inhibitor UV-4. These host-targeting compounds are candidates for investigation in animal models of SARS-CoV-2 and for testing against other viruses that rely on ERQC for correct glycoprotein folding.
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Affiliation(s)
- Sharanbasappa S. Karade
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Evelyn J. Franco
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Ana C. Rojas
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Kaley C. Hanrahan
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Alexander Kolesnikov
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Wenbo Yu
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Alexander D. MacKerell
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | | | - David J. Weber
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Ashley N. Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Anthony M. Treston
- Emergent BioSolutions, Gaithersburg, MD 20879, USA
- Current address: Treadwell Therapeutics, Toronto M5G 2M9, Canada
| | - Roy A. Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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11
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Wang Q, Meng F, Xie Y, Wang W, Meng Y, Li L, Liu T, Qi J, Ni X, Zheng S, Huang J, Huang N. In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein. ACS CENTRAL SCIENCE 2023; 9:252-265. [PMID: 36844485 PMCID: PMC9924089 DOI: 10.1021/acscentsci.2c01190] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Indexed: 05/27/2023]
Abstract
The spike protein of SARS-CoV-2 has been a promising target for developing vaccines and therapeutics due to its crucial role in the viral entry process. Previously reported cryogenic electron microscopy (cryo-EM) structures have revealed that free fatty acids (FFA) bind with SARS-CoV-2 spike protein, stabilizing its closed conformation and reducing its interaction with the host cell target in vitro. Inspired by these, we utilized a structure-based virtual screening approach against the conserved FFA-binding pocket to identify small molecule modulators of SARS-CoV-2 spike protein, which helped us identify six hits with micromolar binding affinities. Further evaluation of their commercially available and synthesized analogs enabled us to discover a series of compounds with better binding affinities and solubilities. Notably, our identified compounds exhibited similar binding affinities against the spike proteins of the prototypic SARS-CoV-2 and a currently circulating Omicron BA.4 variant. Furthermore, the cryo-EM structure of the compound SPC-14 bound spike revealed that SPC-14 could shift the conformational equilibrium of the spike protein toward the closed conformation, which is human ACE2 (hACE2) inaccessible. Our identified small molecule modulators targeting the conserved FFA-binding pocket could serve as the starting point for the future development of broad-spectrum COVID-19 intervention treatments.
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Affiliation(s)
- Qing Wang
- School
of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Fanhao Meng
- Shuimu
Biosciences, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Yuting Xie
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Wei Wang
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Yumin Meng
- CAS
Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Linjie Li
- CAS
Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Liu
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Jianxun Qi
- CAS
Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaodan Ni
- Shuimu
Biosciences, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
| | - Sanduo Zheng
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Jianhui Huang
- School
of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Niu Huang
- National
Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, No. 7 Science Park Road, Beijing 102206, China
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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12
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Zhekova HR, Jiang J, Wang W, Tsirulnikov K, Kayık G, Khan HM, Azimov R, Abuladze N, Kao L, Newman D, Noskov SY, Tieleman DP, Hong Zhou Z, Pushkin A, Kurtz I. CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations. Commun Biol 2022; 5:1372. [PMID: 36517642 PMCID: PMC9751308 DOI: 10.1038/s42003-022-04306-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Jiansen Jiang
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Weiguang Wang
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Kirill Tsirulnikov
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Gülru Kayık
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Hanif Muhammad Khan
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rustam Azimov
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalia Abuladze
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Liyo Kao
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Debbie Newman
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Alexander Pushkin
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ira Kurtz
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Brain Research Institute, University of California, Los Angeles, CA, USA.
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13
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In silico identification of a β 2-adrenoceptor allosteric site that selectively augments canonical β 2AR-Gs signaling and function. Proc Natl Acad Sci U S A 2022; 119:e2214024119. [PMID: 36449547 PMCID: PMC9894167 DOI: 10.1073/pnas.2214024119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and other obstructive lung diseases. However, the therapeutic efficacy of β-agonists is limited by agonist-induced β2AR desensitization and noncanonical β2AR signaling involving β-arrestin that is shown to promote asthma pathophysiology. Accordingly, we undertook the identification of an allosteric site on β2AR that could modulate the activity of β-agonists to overcome these limitations. We employed the site identification by ligand competitive saturation (SILCS) computational method to comprehensively map the entire 3D structure of in silico-generated β2AR intermediate conformations and identified a putative allosteric binding site. Subsequent database screening using SILCS identified drug-like molecules with the potential to bind to the site. Experimental assays in HEK293 cells (expressing recombinant wild-type human β2AR) and human ASM cells (expressing endogenous β2AR) identified positive and negative allosteric modulators (PAMs and NAMs) of β2AR as assessed by regulation of β-agonist-stimulation of cyclic AMP generation. PAMs/NAMs had no effect on β-agonist-induced recruitment of β-arrestin to β2AR- or β-agonist-induced loss of cell surface expression in HEK293 cells expressing β2AR. Mutagenesis analysis of β2AR confirmed the SILCS identified site based on mutants of amino acids R131, Y219, and F282. Finally, functional studies revealed augmentation of β-agonist-induced relaxation of contracted human ASM cells and bronchodilation of contracted airways. These findings identify a allosteric binding site on the β2AR, whose activation selectively augments β-agonist-induced Gs signaling, and increases relaxation of ASM cells, the principal therapeutic effect of β-agonists.
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14
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Chong G, MacKerell AD. Spatial requirements for ITAM signaling in an intracellular natural killer cell model membrane. Biochim Biophys Acta Gen Subj 2022; 1866:130221. [PMID: 35933027 PMCID: PMC9420803 DOI: 10.1016/j.bbagen.2022.130221] [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: 04/29/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/17/2022]
Abstract
FcγRIIIa-FcεRIγ complexes, upon stimulation by antibodies, cluster to initiate intracellular signaling and activate natural killer (NK) cells. Intracellular signaling involves Lck phosphorylation of ITAMs of each monomer of a FcεRIγ homodimer in a FcγRIIIa-FcεRIγ complex and subsequent binding of two phosphotyrosines (pY) in tandem by a Syk family kinase. However, how FcR clustering triggers ITAM signaling is not resolved. Molecular modeling and dynamics (MD) simulations are applied to generate ensembles of structures of the FcγRIIIa and FcεRIγ homodimeric cytoplasmic tails of FcγRIIIa-FcεRIγ complexes based on the transmembrane helices and cytoplasmic tails spaced 120, 80, and 50 Å apart to model different extents of clustering. Site-identification by ligand competitive saturation method with Monte Carlo sampling (SILCS-MC) is used to model how Lck could phosphorylate a diversity of ITAM conformations. At 80 Å separation between FcγRIIIa-FcεRIγ complexes, Lck can perform multiple phosphorylations on individual and multiple ITAMs across complexes, including potential sequential phosphorylation events. Syk may then potentially bind the two pYs within a single ITAM in tandem in isolated FcγRIIIa-FcεRIγ complexes, as observed in CD3ε and ζ chains of T cell receptors by the Syk family kinase ZAP-70. In addition, at 50 Å separation between complexes, unique to natural killer cells over T cells, Syk could potentially bind in tandem to pYs in different ITAMs across FcγRIIIa-FcεRIγ complexes. Thus, we predict that an ensemble of spatial orientations of the ITAMS of FcγRIIIa-FcεRIγ complexes that occur upon clustering lead to ITAM phosphorylation by Lck and subsequent Syk activity thereby facilitating downstream signaling.
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Affiliation(s)
- Gene Chong
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, United States
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, United States.
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15
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Kognole AA, Hazel A, MacKerell AD. SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules. J Chem Theory Comput 2022; 18:5672-5691. [PMID: 35913731 PMCID: PMC9474704 DOI: 10.1021/acs.jctc.2c00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules can act as potential drug targets in different diseases, as their dysregulated expression or misfolding can alter various cellular processes. Noncoding RNAs account for ∼70% of the human genome, and these molecules can have complex tertiary structures that present a great opportunity for targeting by small molecules. In the present study, the site identification by ligand competitive saturation (SILCS) computational approach is extended to target RNA, termed SILCS-RNA. Extensions to the method include an enhanced oscillating excess chemical potential protocol for the grand canonical Monte Carlo calculations and individual simulations of the neutral and charged solutes from which the SILCS functional group affinity maps (FragMaps) are calculated for subsequent binding site identification and docking calculations. The method is developed and evaluated against seven RNA targets and their reported small molecule ligands. SILCS-RNA provides a detailed characterization of the functional group affinity pattern in the small molecule binding sites, recapitulating the types of functional groups present in the ligands. The developed method is also shown to be useful for identification of new potential binding sites and identifying ligand moieties that contribute to binding, granular information that can facilitate ligand design. However, limitations in the method are evident including the ability to map the regions of binding sites occupied by ligand phosphate moieties and to fully account for the wide range of conformational heterogeneity in RNA associated with binding of different small molecules, emphasizing inherent challenges associated with applying computer-aided drug design methods to RNA. While limitations are present, the current study indicates how the SILCS-RNA approach may enhance drug discovery efforts targeting RNAs with small molecules.
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Affiliation(s)
- Abhishek A Kognole
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
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16
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Goel H, Yu W, MacKerell AD. hERG Blockade Prediction by Combining Site Identification by Ligand Competitive Saturation and Physicochemical Properties. CHEMISTRY (BASEL, SWITZERLAND) 2022; 4:630-646. [PMID: 36712295 PMCID: PMC9881610 DOI: 10.3390/chemistry4030045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human ether-a-go-go-related gene (hERG) potassium channel is well-known contributor to drug-induced cardiotoxicity and therefore an extremely important target when performing safety assessments of drug candidates. Ligand-based approaches in connection with quantitative structure active relationships (QSAR) analyses have been developed to predict hERG toxicity. Availability of the recent published cryogenic electron microscopy (cryo-EM) structure for the hERG channel opened the prospect for using structure-based simulation and docking approaches for hERG drug liability predictions. In recent time, the idea of combining structure- and ligand-based approaches for modeling hERG drug liability has gained momentum offering improvements in predictability when compared to ligand-based QSAR practices alone. The present article demonstrates uniting the structure-based SILCS (site-identification by ligand competitive saturation) approach in conjunction with physicochemical properties to develop predictive models for hERG blockade. This combination leads to improved model predictability based on Pearson's R and percent correct (represents rank-ordering of ligands) metric for different validation sets of hERG blockers involving diverse chemical scaffold and wide range of pIC50 values. The inclusion of the SILCS structure-based approach allows determination of the hERG region to which compounds bind and the contribution of different chemical moieties in the compounds to blockade, thereby facilitating the rational ligand design to minimize hERG liability.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
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17
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Tze-Yang Ng J, Tan YS. Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites. J Chem Theory Comput 2022; 18:1969-1981. [PMID: 35175753 DOI: 10.1021/acs.jctc.1c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification and characterization of binding sites is a critical component of structure-based drug design (SBDD). Probe-based/cosolvent molecular dynamics (MD) methods that allow for protein flexibility have been developed to predict ligand binding sites. However, cryptic pockets that appear only upon ligand binding and occluded binding sites with no access to the solvent pose significant challenges to these methods. Here, we report the development of accelerated ligand-mapping MD (aLMMD), which combines accelerated MD with LMMD, for the detection of these challenging binding sites. The method was validated on five proteins with what we term "recalcitrant" cryptic pockets, which are deeply buried pockets that require extensive movement of the protein backbone to expose, and three proteins with occluded binding sites. In all the cases, aLMMD was able to detect and sample the binding sites. Our results suggest that aLMMD could be used as a general approach for the detection of such elusive binding sites in protein targets, thus providing valuable information for SBDD.
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Affiliation(s)
- Justin Tze-Yang Ng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
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18
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Goel H, Hazel A, Yu W, Jo S, MacKerell AD. Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design. NEW J CHEM 2022; 46:919-932. [PMID: 35210743 PMCID: PMC8863107 DOI: 10.1039/d1nj04028f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Site Identification by Ligand Competitive Saturation (SILCS) is a molecular simulation approach that uses diverse small solutes in aqueous solution to obtain functional group affinity patterns of a protein or other macromolecule. This involves employing a combined Grand Canonical Monte Carlo (GCMC)-molecular dynamics (MD) method to sample the full 3D space of the protein, including deep binding pockets and interior cavities from which functional group free energy maps (FragMaps) are obtained. The information content in the maps, which include contributions from protein flexibilty and both protein and functional group desolvation contributions, can be used in many aspects of the drug discovery process. These include identification of novel ligand binding pockets, including allosteric sites, pharmacophore modeling, prediction of relative protein-ligand binding affinities for database screening and lead optimization efforts, evaluation of protein-protein interactions as well as in the formulation of biologics-based drugs including monoclonal antibodies. The present article summarizes the various tools developed in the context of the SILCS methodology and their utility in computer-aided drug design (CADD) applications, showing how the SILCS toolset can improve the drug-development process on a number of fronts with respect to both accuracy and throughput representing a new avenue of CADD applications.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States
| | - Sunhwan Jo
- SilcsBio LLC, 1100 Wicomico St. Suite 323, Baltimore, MD, 21230, United States
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States., SilcsBio LLC, 1100 Wicomico St. Suite 323, Baltimore, MD, 21230, United States.,, Tel: 410-706-7442, Fax: 410-706-5017
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19
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Wang W, Tsirulnikov K, Zhekova HR, Kayık G, Khan HM, Azimov R, Abuladze N, Kao L, Newman D, Noskov SY, Zhou ZH, Pushkin A, Kurtz I. Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE. Nat Commun 2021; 12:5690. [PMID: 34584093 PMCID: PMC8478935 DOI: 10.1038/s41467-021-25998-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) transporters revealed an identical overall fold despite their different transport modes (chloride/bicarbonate exchange versus sodium-carbonate cotransport). However, the exact mechanism determining the different transport modes in the SLC4 family remains unknown. In this work, we report the cryo-EM 3.4 Å structure of the OF conformation of NDCBE (SLC4A8), which shares transport properties with both AE1 and NBCe1 by mediating the electroneutral exchange of sodium-carbonate with chloride. This structure features a fully resolved extracellular loop 3 and well-defined densities corresponding to sodium and carbonate ions in the tentative substrate binding pocket. Further, we combine computational modeling with functional studies to unravel the molecular determinants involved in NDCBE and SLC4 transport.
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Affiliation(s)
- Weiguang Wang
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.509979.b0000 0004 7666 6191Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA USA
| | - Kirill Tsirulnikov
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Hristina R. Zhekova
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Gülru Kayık
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Hanif Muhammad Khan
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rustam Azimov
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Natalia Abuladze
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Liyo Kao
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Debbie Newman
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Sergei Yu. Noskov
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Z. Hong Zhou
- grid.509979.b0000 0004 7666 6191Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA USA
| | - Alexander Pushkin
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Ira Kurtz
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Brain Research Institute, University of California, Los Angeles, CA USA
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20
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Goel H, Hazel A, Ustach VD, Jo S, Yu W, MacKerell AD. Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation. Chem Sci 2021; 12:8844-8858. [PMID: 34257885 PMCID: PMC8246086 DOI: 10.1039/d1sc01781k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/24/2021] [Indexed: 01/18/2023] Open
Abstract
Predicting relative protein-ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design. The site identification by ligand competitive saturation (SILCS) methodology is based on functional group affinity patterns in the form of free energy maps that may be used to compute protein-ligand binding poses and affinities. Presented are results obtained from the SILCS methodology for a set of eight target proteins as reported originally in Wang et al. (J. Am. Chem. Soc., 2015, 137, 2695-2703) using free energy perturbation (FEP) methods in conjunction with enhanced sampling and cycle closure corrections. These eight targets have been subsequently studied by many other authors to compare the efficacy of their method while comparing with the outcomes of Wang et al. In this work, we present results for a total of 407 ligands on the eight targets and include specific analysis on the subset of 199 ligands considered previously. Using the SILCS methodology we can achieve an average accuracy of up to 77% and 74% when considering the eight targets with their 199 and 407 ligands, respectively, for rank-ordering ligand affinities as calculated by the percent correct metric. This accuracy increases to 82% and 80%, respectively, when the SILCS atomic free energy contributions are optimized using a Bayesian Markov-chain Monte Carlo approach. We also report other metrics including Pearson's correlation coefficient, Pearlman's predictive index, mean unsigned error, and root mean square error for both sets of ligands. The results obtained for the 199 ligands are compared with the outcomes of Wang et al. and other published works. Overall, the SILCS methodology yields similar or better-quality predictions without a priori need for known ligand orientations in terms of the different metrics when compared to current FEP approaches with significant computational savings while additionally offering quantitative estimates of individual atomic contributions to binding free energies. These results further validate the SILCS methodology as an accurate, computationally efficient tool to support lead optimization and drug discovery.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Vincent D Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Sunhwan Jo
- SilcsBio LLC 8 Market Place, Suite 300 Baltimore Maryland 21201 USA
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
- SilcsBio LLC 8 Market Place, Suite 300 Baltimore Maryland 21201 USA
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21
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Identification of multiple substrate binding sites in SLC4 transporters in the outward-facing conformation: Insights into the transport mechanism. J Biol Chem 2021; 296:100724. [PMID: 33932403 PMCID: PMC8191340 DOI: 10.1016/j.jbc.2021.100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 01/17/2023] Open
Abstract
Solute carrier family 4 (SLC4) transporters mediate the transmembrane transport of HCO3-, CO32-, and Cl- necessary for pH regulation, transepithelial H+/base transport, and ion homeostasis. Substrate transport with varying stoichiometry and specificity is achieved through an exchange mechanism and/or through coupling of the uptake of anionic substrates to typically co-transported Na+. Recently solved outward-facing structures of two SLC4 members (human anion exchanger 1 [hAE1] and human electrogenic sodium bicarbonate cotransporter 1 [hNBCe1]) with different transport modes (Cl-/HCO3- exchange versus Na+-CO32- symport) revealed highly conserved three-dimensional organization of their transmembrane domains. However, the exact location of the ion binding sites and their protein-ion coordination motifs are still unclear. In the present work, we combined site identification by ligand competitive saturation mapping and extensive molecular dynamics sampling with functional mutagenesis studies which led to the identification of two substrate binding sites (entry and central) in the outward-facing states of hAE1 and hNBCe1. Mutation of residues in the identified binding sites led to impaired transport in both proteins. We also showed that R730 in hAE1 is crucial for anion binding in both entry and central sites, whereas in hNBCe1, a Na+ acts as an anchor for CO32- binding to the central site. Additionally, protonation of the central acidic residues (E681 in hAE1 and D754 in hNBCe1) alters the ion dynamics in the permeation cavity and may contribute to the transport mode differences in SLC4 proteins. These results provide a basis for understanding the functional differences between hAE1 and hNBCe1 and may facilitate potential drug development for diseases such as proximal and distal renal tubular acidosis.
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22
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Lind C, Pandey P, Pastor RW, MacKerell AD. Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation. J Chem Theory Comput 2021; 17:3188-3202. [PMID: 33929848 DOI: 10.1021/acs.jctc.1c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules such as metabolites and drugs must pass through the membrane of the cell, a barrier primarily comprising phospholipid bilayers and embedded proteins. To better understand the process of passive diffusion, knowledge of the ability of various functional groups to partition across bilayers and the associated energetics would be of utility. In the present study, the site identification by ligand competitive saturation (SILCS) methodology has been applied to sample the distributions of a diverse set of chemical solutes representing the functional groups of small molecules across phospholipid bilayers composed of 0.9:0.1 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/cholesterol and a mixture of 0.52:0.18:0.3 1,2-dioleoyl-sn-glycero-3-phospho-l-serine/1,2-dioleoyl-sn-glycero-3-phosphocholine/cholesterol used in parallel artificial membrane permeability assay experiments. A combination of oscillating chemical potential grand canonical Monte Carlo and molecular dynamics in the SILCS simulations was applied to achieve solute sampling through the bilayers and surrounding aqueous environment from which the distribution of solutes and the functional groups they represent were obtained. Results show differential distribution of aliphatic versus aromatic groups with the former having increased sampling in the center of the bilayers versus in the region of the glycerol linker for the latter. Variations in the distribution of different polar groups are evident, with large differences between negative acetate and positive methylammonium with accumulation of the polar-neutral and acetate solutes above the bilayer head groups. Conversion of the distributions to absolute free energies allows for a detailed understanding of energetics of functional groups in different regions of the bilayers and for calculation of absolute free-energy profiles of multifunctional drug-like molecules across the bilayers from which partition coefficients and resistance factors suitable for insertion into the homogenous solubility-diffusion equation for calculation of permeability were obtained. Comparisons of the calculated bilayer/solution partition coefficients with 1-octanol/water experimental data for both drug-like molecules and the solutes show overall good agreement, validating the calculated distributions and associated absolute free-energy profiles.
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Affiliation(s)
- Christoffer Lind
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Poonam Pandey
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
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23
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A Gomes A, da Silva GF, Lakkaraju SK, Guimarães BG, MacKerell AD, Magalhães MDLB. Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A. J Chem Inf Model 2021; 61:1931-1941. [PMID: 33819021 DOI: 10.1021/acs.jcim.0c01450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Second-generation ethanol production involves the use of agricultural and forestry waste as feedstock, being an alternative to the first-generation technology as it relies on low-cost abundant residues and does not affect food agriculture. However, the success of second-generation biorefineries relies on energetically efficient processes and effective enzyme cocktails to convert cellulose into fermentable sugars. β-glucosidases catalyze the last step on the enzymatic hydrolysis of cellulose; however, they are often inhibited by glucose. Previous studies demonstrated that glucose-6-phosphate (G6P) is a positive allosteric modulator of Bacillus polymyxa β-glucosidase A, improving enzymatic efficiency, providing thermoresistance, and imparting glucose tolerance. However, the precise molecular details of G6P-β-glucosidase A interactions have not yet been described so far. We investigated the molecular details of G6P binding into B. polymyxa β-glucosidase A through in silico docking using the site identification by ligand competitive saturation technology followed by site-directed mutagenesis studies, from which an allosteric binding site for G6P was identified. In addition, a mechanistic shift toward the transglycosylation reaction as opposed to hydrolysis was observed in the presence of G6P, suggesting a new role of G6P allosteric modulation of the catalytic activity of β-glucosidase A.
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Affiliation(s)
- Anderson A Gomes
- Biochemistry Laboratory, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Gustavo F da Silva
- Biochemistry Laboratory, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Sirish K Lakkaraju
- Small Molecule Drug Discovery, Bristol Myers Squibb, Route 206 & Province Line Road, Princeton, New Jersey 08543, United States
| | - Beatriz Gomes Guimarães
- Laboratory of Structural Biology and Protein Engineering, Instituto Carlos Chagas, FIOCRUZ Paraná, Curitiba, Parana 81350-010, Brazil
| | - Alexander D MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Maria de Lourdes B Magalhães
- Biochemistry Laboratory, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
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24
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Solano-Gonzalez E, Coburn KM, Yu W, Wilson GM, Nurmemmedov E, Kesari S, Chang ET, MacKerell AD, Weber DJ, Carrier F. Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint. Nucleic Acids Res 2021; 49:1235-1246. [PMID: 33398344 PMCID: PMC7897483 DOI: 10.1093/nar/gkaa1254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/01/2022] Open
Abstract
We have identified chemical probes that simultaneously inhibit cancer cell progression and an immune checkpoint. Using the computational Site Identification by Ligand Competitive Saturation (SILCS) technology, structural biology and cell-based assays, we identify small molecules that directly and selectively bind to the RNA Recognition Motif (RRM) of hnRNP A18, a regulator of protein translation in cancer cells. hnRNP A18 recognizes a specific RNA signature motif in the 3′UTR of transcripts associated with cancer cell progression (Trx, VEGF, RPA) and, as shown here, a tumor immune checkpoint (CTLA-4). Post-transcriptional regulation of immune checkpoints is a potential therapeutic strategy that remains to be exploited. The probes target hnRNP A18 RRM in vitro and in cells as evaluated by cellular target engagement. As single agents, the probes specifically disrupt hnRNP A18–RNA interactions, downregulate Trx and CTLA-4 protein levels and inhibit proliferation of several cancer cell lines without affecting the viability of normal epithelial cells. These first-in-class chemical probes will greatly facilitate the elucidation of the underexplored biological function of RNA Binding Proteins (RBPs) in cancer cells, including their effects on proliferation and immune checkpoint activation.
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Affiliation(s)
- Eduardo Solano-Gonzalez
- University of Maryland, Baltimore, School of Medicine, Department of Radiation Oncology, 655 West Baltimore, Street, Baltimore, MD 21201, USA
| | - Katherine M Coburn
- University of Maryland, Baltimore, School of Medicine, Department of Biochemistry and Molecular Biology, 108 N. Greene Street, Baltimore, MD 21201, USA
| | - Wenbo Yu
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore MD 21201, USA.,Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Gerald M Wilson
- University of Maryland, Baltimore, School of Medicine, Department of Biochemistry and Molecular Biology, 108 N. Greene Street, Baltimore, MD 21201, USA
| | - Elmar Nurmemmedov
- John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
| | - Santosh Kesari
- John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
| | - Elizabeth T Chang
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - Alexander D MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore MD 21201, USA.,Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David J Weber
- University of Maryland, Baltimore, School of Medicine, Department of Biochemistry and Molecular Biology, 108 N. Greene Street, Baltimore, MD 21201, USA.,University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA.,Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - France Carrier
- University of Maryland, Baltimore, School of Medicine, Department of Radiation Oncology, 655 West Baltimore, Street, Baltimore, MD 21201, USA.,University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
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25
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Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des 2021; 35:167-177. [PMID: 32968887 PMCID: PMC7904576 DOI: 10.1007/s10822-020-00344-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022]
Abstract
Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment to relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our BLUES (NCMC/MD) method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.
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Affiliation(s)
| | - Ido Y Ben-Shalom
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nathan M Lim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Sam C Gill
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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26
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Parvaiz N, Ahmad F, Yu W, MacKerell AD, Azam SS. Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae. PLoS One 2021; 16:e0244967. [PMID: 33449932 PMCID: PMC7810305 DOI: 10.1371/journal.pone.0244967] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
β-lactam antibiotics are the most widely used antimicrobial agents since the discovery of benzylpenicillin in the 1920s. Unfortunately, these life-saving antibiotics are vulnerable to inactivation by continuously evolving β-lactamase enzymes that are primary resistance determinants in multi-drug resistant pathogens. The current study exploits the strategy of combination therapeutics and aims at identifying novel β-lactamase inhibitors that can inactivate the β-lactamase enzyme of the pathogen while allowing the β-lactam antibiotic to act against its penicillin-binding protein target. Inhibitor discovery applied the Site-Identification by Ligand Competitive Saturation (SILCS) technology to map the functional group requirements of the β-lactamase CMY-10 and generate pharmacophore models of active site. SILCS-MC, Ligand-grid Free Energy (LGFE) analysis and Machine-learning based random-forest (RF) scoring methods were then used to screen and filter a library of 700,000 compounds. From the computational screens 74 compounds were subjected to experimental validation in which β-lactamase activity assay, in vitro susceptibility testing, and Scanning Electron Microscope (SEM) analysis were conducted to explore their antibacterial potential. Eleven compounds were identified as enhancers while 7 compounds were recognized as inhibitors of CMY-10. Of these, compound 11 showed promising activity in β-lactamase activity assay, in vitro susceptibility testing against ATCC strains (E. coli, E. cloacae, E. agglomerans, E. alvei) and MDR clinical isolates (E. cloacae, E. alvei and E. agglomerans), with synergistic assay indicating its potential as a β-lactam enhancer and β-lactamase inhibitor. Structural similarity search against the active compound 11 yielded 28 more compounds. The majority of these compounds also exhibited β-lactamase inhibition potential and antibacterial activity. The non-β-lactam-based β-lactamase inhibitors identified in the current study have the potential to be used in combination therapy with lactam-based antibiotics against MDR clinical isolates that have been found resistant against last-line antibiotics.
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Affiliation(s)
- Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wenbo Yu
- University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, United States of America
| | - Alexander D. MacKerell
- University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, United States of America
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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27
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Young BD, Yu W, Rodríguez DJV, Varney KM, MacKerell AD, Weber DJ. Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS). Molecules 2021; 26:E381. [PMID: 33450915 PMCID: PMC7828390 DOI: 10.3390/molecules26020381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/29/2022] Open
Abstract
S100B, a biomarker of malignant melanoma, interacts with the p53 protein and diminishes its tumor suppressor function, which makes this S100 family member a promising therapeutic target for treating malignant melanoma. However, it is a challenge to design inhibitors that are specific for S100B in melanoma versus other S100-family members that are important for normal cellular activities. For example, S100A1 is most similar in sequence and structure to S100B, and this S100 protein is important for normal skeletal and cardiac muscle function. Therefore, a combination of NMR and computer aided drug design (CADD) was used to initiate the design of specific S100B inhibitors. Fragment-based screening by NMR, also termed "SAR by NMR," is a well-established method, and was used to examine spectral perturbations in 2D [1H, 15N]-HSQC spectra of Ca2+-bound S100B and Ca2+-bound S100A1, side-by-side, and under identical conditions for comparison. Of the 1000 compounds screened, two were found to be specific for binding Ca2+-bound S100A1 and four were found to be specific for Ca2+-bound S100B, respectively. The NMR spectral perturbations observed in these six data sets were then used to model how each of these small molecule fragments showed specificity for one S100 versus the other using a CADD approach termed Site Identification by Ligand Competitive Saturation (SILCS). In summary, the combination of NMR and computational approaches provided insight into how S100A1 versus S100B bind small molecules specifically, which will enable improved drug design efforts to inhibit elevated S100B in melanoma. Such a fragment-based approach can be used generally to initiate the design of specific inhibitors for other highly homologous drug targets.
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Affiliation(s)
- Brianna D. Young
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
| | - Wenbo Yu
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - Darex J. Vera Rodríguez
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - Alexander D. MacKerell
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - David J. Weber
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
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28
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Mousaei M, Kudaibergenova M, MacKerell AD, Noskov S. Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. J Chem Inf Model 2020; 60:6489-6501. [PMID: 33196188 PMCID: PMC7839320 DOI: 10.1021/acs.jcim.0c01065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug-induced cardiotoxicity is a potentially lethal and yet one of the most common side effects with the drugs in clinical use. Most of the drug-induced cardiotoxicity is associated with an off-target pharmacological blockade of K+ currents carried out by the cardiac Human-Ether-a-go-go-Related (hERG1) potassium channel. There is a compulsory preclinical stage safety assessment for the hERG1 blockade for all classes of drugs, which adds substantially to the cost of drug development. The availability of a high-resolution cryogenic electron microscopy (cryo-EM) structure for the channel in its open/depolarized state solved in 2017 enabled the application of molecular modeling for rapid assessment of drug blockade by molecular docking and simulation techniques. More importantly, if successful, in silico methods may allow a path to lead-compound salvaging by mapping out key block determinants. Here, we report the blind application of the site identification by the ligand competitive saturation (SILCS) protocol to map out druggable/regulatory hotspots in the hERG1 channel available for blockers and activators. The SILCS simulations use small solutes representative of common functional groups to sample the chemical space for the entire protein and its environment using all-atom simulations. The resulting chemical maps, FragMaps, explicitly account for receptor flexibility, protein-fragment interactions, and fragment desolvation penalty allowing for rapid ranking of potential ligands as blockers or nonblockers of hERG1. To illustrate the power of the approach, SILCS was applied to a test set of 55 blockers with diverse chemical scaffolds and pIC50 values measured under uniform conditions. The original SILCS model was based on the all-atom modeling of the hERG1 channel in an explicit lipid bilayer and was further augmented with a Bayesian-optimization/machine-learning (BML) stage employing an independent literature-derived training set of 163 molecules. BML approach was used to determine weighting factors for the FragMaps contributions to the scoring function. pIC50 predictions from the combined SILCS/BML approach to the 55 blockers showed a Pearson correlation (PC) coefficient of >0.535 relative to the experimental data. SILCS/BML model was shown to yield substantially improved performance as compared to commonly used rigid and flexible molecular docking methods for a well-established cohort of hERG1 blockers, where no correlation with experimental data was recorded. SILCS/BML results also suggest that a proper weighting of protonation states of common blockers present at physiological pH is essential for accurate predictions of blocker potency. The precalculated and optimized SILCS FragMaps can now be used for the rapid screening of small molecules for their cardiotoxic potential as well as for exploring alternative binding pockets in the hERG1 channel with applications to the rational design of activators.
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Affiliation(s)
- Mahdi Mousaei
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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29
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Jo S, Xu A, Curtis JE, Somani S, MacKerell AD. Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection Using the Site Identification by Ligand Competitive Saturation-Biologics Approach. Mol Pharm 2020; 17:4323-4333. [PMID: 32965126 DOI: 10.1021/acs.molpharmaceut.0c00775] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein therapeutics typically require a concentrated protein formulation, which can lead to self-association and/or high viscosity due to protein-protein interaction (PPI). Excipients are often added to improve stability, bioavailability, and manufacturability of the protein therapeutics, but the selection of excipients often relies on trial and error. Therefore, understanding the excipient-protein interaction and its effect on non-specific PPI is important for rational selection of formulation development. In this study, we validate a general workflow based on the site identification by ligand competitive saturation (SILCS) technology, termed SILCS-Biologics, that can be applied to protein therapeutics for rational excipient selection. The National Institute of Standards and Technology monoclonal antibody (NISTmAb) reference along with the CNTO607 mAb is used as model antibody proteins to examine PPIs, and NISTmAb was used to further examine excipient-protein interactions, in silico. Metrics from SILCS include the distribution and predicted affinity of excipients, buffer interactions with the NISTmAb Fab, and the relation of the interactions to predicted PPI. Comparison with a range of experimental data showed multiple SILCS metrics to be predictive. Specifically, the number of favorable sites to which an excipient binds and the number of sites to which an excipient binds that are involved in predicted PPIs correlate with the experimentally determined viscosity. In addition, a combination of the number of binding sites and the predicted binding affinity is indicated to be predictive of relative protein stability. Comparison of arginine, trehalose, and sucrose, all of which give the highest viscosity in combination with analysis of B22 and kD and the SILCS metrics, indicates that higher viscosities are associated with a low number of predicted binding sites, with lower binding affinity of arginine leading to its anomalously high impact on viscosity. The present study indicates the potential for the SILCS-Biologics approach to be of utility in the rational design of excipients during biologics formulation.
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Affiliation(s)
- Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, Maryland 21202, United States
| | - Amy Xu
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Sandeep Somani
- Discovery Sciences, Janssen Research and Development (Janssen R&D), Spring House, Pennsylvania 19477, United States
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United States
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30
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Somani S, Jo S, Thirumangalathu R, Rodrigues D, Tanenbaum LM, Amin K, MacKerell AD, Thakkar SV. Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS). J Pharm Sci 2020; 110:1103-1110. [PMID: 33137372 DOI: 10.1016/j.xphs.2020.10.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Formulation of protein-based therapeutics employ advanced formulation and analytical technologies for screening various parameters such as buffer, pH, and excipients. At a molecular level, physico-chemical properties of a protein formulation depend on self-interaction between protein molecules, protein-solvent and protein-excipient interactions. This work describes a novel in silico approach, SILCS-Biologics, for structure-based modeling of protein formulations. SILCS Biologics is based on the Site-Identification by Ligand Competitive Saturation (SILCS) technology and enables modeling of interactions among different components of a formulation at an atomistic level while accounting for protein flexibility. It predicts potential hotspot regions on the protein surface for protein-protein and protein-excipient interactions. Here we apply SILCS-Biologics on a Fab domain of a monoclonal antibody (mAbN) to model Fab-Fab interactions and interactions with three amino acid excipients, namely, arginine HCl, proline and lysine HCl. Experiments on 100 mg/ml formulations of mAbN showed that arginine increased, lysine reduced, and proline did not impact viscosity. We use SILCS-Biologics modeling to explore a structure-based hypothesis for the viscosity modulating effect of these excipients. Current efforts are aimed at further validation of this novel computational framework and expanding the scope to model full mAb and other protein therapeutics.
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Affiliation(s)
- Sandeep Somani
- Discovery Sciences, Janssen Research and Development (Janssen R&D), Spring House, PA 19477, USA
| | | | - Renuka Thirumangalathu
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Danika Rodrigues
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Laura M Tanenbaum
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Ketan Amin
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Alexander D MacKerell
- SilcsBio LLC, Baltimore, MD 21202, USA; Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
| | - Santosh V Thakkar
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA; BioTherapeutics Cell and Developability Sciences (BioTD CDS), Janssen Research and Development (Janssen R&D), Spring House, PA 19477, USA.
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31
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Kognole AA, MacKerell AD. Contributions and competition of Mg 2+ and K + in folding and stabilization of the Twister ribozyme. RNA (NEW YORK, N.Y.) 2020; 26:1704-1715. [PMID: 32769092 PMCID: PMC7566569 DOI: 10.1261/rna.076851.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg2+ in a background of monovalent ions. In a recent study, we have shown how the presence of Mg2+ impacts the transition from partially unfolded to folded states through a "push-pull" mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To further understand the ion atmosphere of RNA in folded and partially folded states results from atomistic umbrella sampling and oscillating chemical potential grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg2+ and K+ ions around Twister RNA. Results show the presence of 100 mM Mg2+ to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states, overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K+ ions. Furthermore, K+ preferentially interacts with purine N7 atoms of helical regions in partially unfolded states, thereby potentially stabilizing the helical regions. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K+ can act as a surrogate for Mg2+ by participating in specific interactions with nonsequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at submillimolar Mg2+ concentrations.
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Affiliation(s)
- Abhishek A Kognole
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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32
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Deflorian F, Perez-Benito L, Lenselink EB, Congreve M, van Vlijmen HWT, Mason JS, Graaf CD, Tresadern G. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. J Chem Inf Model 2020; 60:5563-5579. [PMID: 32539374 DOI: 10.1021/acs.jcim.0c00449] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The computational prediction of relative binding free energies is a crucial goal for drug discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug target class. However, they present increased complexity to model compared to soluble globular proteins. Despite breakthroughs, experimental X-ray crystal and cryo-EM structures are challenging to attain, meaning computational models of the receptor and ligand binding mode are sometimes necessary. This leads to uncertainty in understanding ligand-protein binding induced changes such as, water positioning and displacement, side chain positioning, hydrogen bond networks, and the overall structure of the hydration shell around the ligand and protein. In other words, the very elements that define structure activity relationships (SARs) and are crucial for accurate binding free energy calculations are typically more uncertain for GPCRs. In this work we use free energy perturbation (FEP) to predict the relative binding free energies for ligands of two different GPCRs. We pinpoint the key aspects for success such as the important role of key water molecules, amino acid ionization states, and the benefit of equilibration with specific ligands. Initial calculations following typical FEP setup and execution protocols delivered no correlation with experiment, but we show how results are improved in a logical and systematic way. This approach gave, in the best cases, a coefficient of determination (R2) compared with experiment in the range of 0.6-0.9 and mean unsigned errors compared to experiment of 0.6-0.7 kcal/mol. We anticipate that our findings will be applicable to other difficult-to-model protein ligand data sets and be of wide interest for the community to continue improving FE binding energy predictions.
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Affiliation(s)
- Francesca Deflorian
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300, RA, The Netherlands
| | - Miles Congreve
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Herman W T van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Jonathan S Mason
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
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33
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Li G, Zhang W, Xie Y, Li Y, Cao R, Zheng G, Huang N, Zhou Y. Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors. J Chem Inf Model 2020; 60:3287-3294. [PMID: 32407627 DOI: 10.1021/acs.jcim.0c00245] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pim-1 kinase has been widely regarded as an attractive target for anticancer drugs. Here, we reported our continued efforts in structure-based optimization of compound 10-DEBC, a previously identified micromolar Pim-1 inhibitor. Guided by the Site Identification by Ligand Competitive Saturation (SILCS) method, we quickly obtained a series of 10-DEBC derivatives with significantly improved activity and selectivity. In particular, compound 26 exhibited an IC50 value of 0.9 nM, as well as 220- and 8-fold selectivity over Pim-2 and Pim-3 kinases, respectively.
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Affiliation(s)
- Gudong Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Zhang
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Yuting Xie
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Yang Li
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Rao Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Niu Huang
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
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Goel H, Yu W, Ustach VD, Aytenfisu AH, Sun D, MacKerell AD. Impact of electronic polarizability on protein-functional group interactions. Phys Chem Chem Phys 2020; 22:6848-6860. [PMID: 32195493 PMCID: PMC7194236 DOI: 10.1039/d0cp00088d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Interactions of proteins with functional groups are key to their biological functions, making it essential that they be accurately modeled. To investigate the impact of the inclusion of explicit treatment of electronic polarizability in force fields on protein-functional group interactions, the additive CHARMM and Drude polarizable force field are compared in the context of the Site-Identification by Ligand Competitive Saturation (SILCS) simulation methodology from which functional group interaction patterns with five proteins for which experimental binding affinities of multiple ligands are available, were obtained. The explicit treatment of polarizability produces significant differences in the functional group interactions in the ligand binding sites including overall enhanced binding of functional groups to the proteins. This is associated with variations of the dipole moments of solutes representative of functional groups in the binding sites relative to aqueous solution with higher dipole moments systematically occurring in the latter, though exceptions occur with positively charged methylammonium. Such variation indicates the complex, heterogeneous nature of the electronic environments of ligand binding sites and emphasizes the inherent limitation of fixed charged, additive force fields for modeling ligand-protein interactions. These effects yield more defined orientation of the functional groups in the binding pockets and a small, but systematic improvement in the ability of the SILCS method to predict the binding orientation and relative affinities of ligands to their target proteins. Overall, these results indicate that the physical model associated with the explicit treatment of polarizability along with the presence of lone pairs in a force field leads to changes in the nature of the interactions of functional groups with proteins versus that occurring with additive force fields, suggesting the utility of polarizable force fields in obtaining a more realistic understanding of protein-ligand interactions.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Vincent D Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Asaminew H Aytenfisu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Delin Sun
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
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35
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Kognole AA, MacKerell AD. Mg 2+ Impacts the Twister Ribozyme through Push-Pull Stabilization of Nonsequential Phosphate Pairs. Biophys J 2020; 118:1424-1437. [PMID: 32053774 PMCID: PMC7091459 DOI: 10.1016/j.bpj.2020.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/23/2019] [Accepted: 01/21/2020] [Indexed: 11/15/2022] Open
Abstract
RNA molecules perform a variety of biological functions for which the correct three-dimensional structure is essential, including as ribozymes where they catalyze chemical reactions. Metal ions, especially Mg2+, neutralize these negatively charged nucleic acids and specifically stabilize RNA tertiary structures as well as impact the folding landscape of RNAs as they assume their tertiary structures. Specific binding sites of Mg2+ in folded conformations of RNA have been studied extensively; however, the full range of interactions of the ion with compact intermediates and unfolded states of RNA is challenging to investigate, and the atomic details of the mechanism by which the ion facilitates tertiary structure formation is not fully known. Here, umbrella sampling combined with oscillating chemical potential Grand Canonical Monte Carlo/molecular dynamics simulations are used to capture the energetics and atomic-level details of Mg2+-RNA interactions that occur along an unfolding pathway of the Twister ribozyme. The free energy profiles reveal stabilization of partially unfolded states by Mg2+, as observed in unfolding experiments, with this stabilization being due to increased sampling of simultaneous interactions of Mg2+ with two or more nonsequential phosphate groups. Notably, these results indicate a push-pull mechanism in which the Mg2+-RNA interactions actually lead to destabilization of specific nonsequential phosphate-phosphate interactions (i.e., pushed apart), whereas other interactions are stabilized (i.e., pulled together), a balance that stabilizes unfolded states and facilitates the folding of Twister, including the formation of hydrogen bonds associated with the tertiary structure. This study establishes a better understanding of how Mg2+-ion interactions contribute to RNA structural properties and stability.
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Affiliation(s)
- Abhishek A Kognole
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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36
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MacKerell AD. Ions Everywhere? Mg 2+ in the μ-Opioid GPCR and Atomic Details of Their Impact on Function. Biophys J 2020; 118:783-784. [PMID: 31676136 DOI: 10.1016/j.bpj.2019.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022] Open
Abstract
Filizola and co-workers have applied a combination of long-time molecular dynamics and oscillating chemical potential grand canonical Monte Carlo/molecular dynamics to investigate the distribution of Mg2+ and Na+ in the μ-opioid receptor and their impact on its function. Results indicate atomic details of potential mechanisms by which Mg2+ leads to increased efficacy of opioid analgesics. The presence of information flow between the extracellular loops and the intracellular region of the G-protein-coupled receptors that interacts with G-proteins in the presence of Mg2+ may be a phenomenon occurring in other G-protein-coupled receptors and, therefore, potentially of broad impact.
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Affiliation(s)
- Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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37
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MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
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Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
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38
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Hu X, Provasi D, Ramsey S, Filizola M. Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation. Biophys J 2019; 118:909-921. [PMID: 31676132 DOI: 10.1016/j.bpj.2019.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 10/08/2019] [Indexed: 01/09/2023] Open
Abstract
In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the μ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na+) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg2+) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. Although ultra-high-resolution opioid receptor crystal structures have revealed a specific Na+ binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg2+ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg2+ and Na+ cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid-water environment and confirmed adequate sampling of Mg2+ ion binding with a grand canonical Monte Carlo MD method. Analyses of these simulations shed light on 1) the preferred binding sites of Mg2+ on the MOP receptor, 2) details of the competition between Mg2+ and Na+ cations for specific sites, 3) estimates of binding affinities, and 4) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg2+ cation.
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Affiliation(s)
- Xiaohu Hu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven Ramsey
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
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Ustach VD, Lakkaraju SK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J Chem Inf Model 2019; 59:3018-3035. [PMID: 31034213 PMCID: PMC6597307 DOI: 10.1021/acs.jcim.9b00210] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical fragment cosolvent sampling techniques have become a versatile tool in ligand-protein binding prediction. Site-identification by ligand competitive saturation (SILCS) is one such method that maps the distribution of chemical fragments on a protein as free energy fields called FragMaps. Ligands are then simulated via Monte Carlo techniques in the field of the FragMaps (SILCS-MC) to predict their binding conformations and relative affinities for the target protein. Application of SILCS-MC using a number of different scoring schemes and MC sampling protocols against multiple protein targets was undertaken to evaluate and optimize the predictive capability of the method. Seven protein targets and 551 ligands with broad chemical variability were used to evaluate and optimize the model to maximize Pearson's correlation coefficient, Pearlman's predictive index, correct relative binding affinity, and root-mean-square error versus the absolute experimental binding affinities. Across the protein-ligand sets, the relative affinities of the ligands were predicted correctly an average of 69% of the time for the highest overall SILCS protocol. Training the FragMap weighting factors using a Bayesian machine learning (ML) algorithm led to an increase to an average 75% relative correct affinity predictions. Furthermore, once the optimal protocol is identified for a specific protein-ligand system average predictabilities of 76% are achieved. The ML algorithm is successful with small training sets of data (30 or more compounds) due to the use of physically correct FragMap weights as priors. Notably, the 76% correct relative prediction rate is similar to or better than free energy perturbation methods that are significantly computationally more expensive than SILCS. The results further support the utility of SILCS as a powerful and computationally accessible tool to support lead optimization and development in drug discovery.
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Affiliation(s)
- Vincent D. Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | | | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Wenjuan Jiang
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202
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40
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Zhang H, Jiang W, Chatterjee P, Luo Y. Ranking Reversible Covalent Drugs: From Free Energy Perturbation to Fragment Docking. J Chem Inf Model 2019; 59:2093-2102. [PMID: 30763080 PMCID: PMC6610880 DOI: 10.1021/acs.jcim.8b00959] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Reversible covalent inhibitors have drawn increasing attention in drug design, as they are likely more potent than noncovalent inhibitors and less toxic than covalent inhibitors. Despite those advantages, the computational prediction of reversible covalent binding presents a formidable challenge because the binding process consists of multiple steps and quantum mechanics (QM) level calculation is needed to estimate the covalent binding free energy. It has been shown that the dissociation rates and the equilibrium dissociation constants vary significantly even with similar warheads, due to noncovalent interactions. We have previously used a simplistic two-state model for predicting the relative binding selectivity of reversible covalent inhibitors ( J. Am. Chem. Soc. 2017, 139 , 17945 ). Here we go beyond binding selectivity and demonstrate that it is possible to use free energy perturbation (FEP) molecular dynamics (MD) to calculate the overall reversible covalent binding using a specially designed thermodynamic cycle. We show that FEP can predict the varying binding free energies of the analogs sharing a common warhead. More importantly, our results revealed that the chemical modification away from warhead alters the binding affinity at both noncovalent and covalent binding states, and the computational prediction can be improved by considering the binding free energy of both states. Furthermore, we explored the possibility of using a more rapid computational method, site-identification by ligand competitive saturation (SILCS), to rank the same set of reversible covalent inhibitors. We found that the fragment docking to a set of precomputed fragment maps produces a reasonable ranking. In conclusion, two independent approaches provided consistent results that the covalent binding state is suitable for the initial ranking of the reversible covalent drug candidates. For lead-optimization, the FEP approach designed here can provide more rigorous and detailed information regarding how much the covalent and noncovalent binding states are contributing to the overall binding affinity, thus offering a new avenue for fine-tuning the noncovalent interactions for optimizing reversible covalent drugs.
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Affiliation(s)
- Han Zhang
- Western University of Health Sciences, College of Pharmacy, Pomona CA 91766
| | - Wenjuan Jiang
- Western University of Health Sciences, College of Pharmacy, Pomona CA 91766
| | - Payal Chatterjee
- Western University of Health Sciences, College of Pharmacy, Pomona CA 91766
| | - Yun Luo
- Western University of Health Sciences, College of Pharmacy, Pomona CA 91766
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Hossain S, Kabedev A, Parrow A, Bergström CAS, Larsson P. Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning. Eur J Pharm Biopharm 2019; 137:46-55. [PMID: 30771454 PMCID: PMC6434319 DOI: 10.1016/j.ejpb.2019.02.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023]
Abstract
In this review we will discuss how computational methods, and in particular classical molecular dynamics simulations, can be used to calculate solubility of pharmaceutically relevant molecules and systems. To the extent possible, we focus on the non-technical details of these calculations, and try to show also the added value of a more thorough and detailed understanding of the solubilization process obtained by using computational simulations. Although the main focus is on classical molecular dynamics simulations, we also provide the reader with some insights into other computational techniques, such as the COSMO-method, and also discuss Flory-Huggins theory and solubility parameters. We hope that this review will serve as a valuable starting point for any pharmaceutical researcher, who has not yet fully explored the possibilities offered by computational approaches to solubility calculations.
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Affiliation(s)
- Shakhawath Hossain
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden
| | - Aleksei Kabedev
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Albin Parrow
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden.
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42
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Aleksandrov A, Myllykallio H. Advances and challenges in drug design against tuberculosis: application of in silico approaches. Expert Opin Drug Discov 2018; 14:35-46. [PMID: 30477360 DOI: 10.1080/17460441.2019.1550482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains the deadliest infectious disease in the world with one-third of the world's population thought to be infected. Over the years, TB mortality rate has been largely reduced; however, this progress has been threatened by the increasing appearance of multidrug-resistant Mtb. Considerable recent efforts have been undertaken to develop new generation antituberculosis drugs. Many of these attempts have relied on in silico approaches, which have emerged recently as powerful tools complementary to biochemical attempts. Areas covered: The authors review the status of pharmaceutical drug development against TB with a special emphasis on computational work. They focus on those studies that have been validated by in vitro and/or in vivo experiments, and thus, that can be considered as successful. The major goals of this review are to present target protein systems, to highlight how in silico efforts compliment experiments, and to aid future drug design endeavors. Expert opinion: Despite having access to all of the gene and protein sequences of Mtb, the search for new optimal treatments against this deadly pathogen are still ongoing. Together with the geometric growth of protein structural and sequence databases, computational methods have become a powerful technique accelerating the successful identification of new ligands.
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Affiliation(s)
- Alexey Aleksandrov
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
| | - Hannu Myllykallio
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
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43
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Sun D, Lakkaraju SK, Jo S, MacKerell AD. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water. J Chem Theory Comput 2018; 14:5290-5302. [PMID: 30183291 DOI: 10.1021/acs.jctc.8b00604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Grand canonical Monte Carlo (GCMC) simulations of ionic solutions with explicit solvent models are known to be challenging. One challenge arises from the treatment of long-range electrostatics and finite-box size in Monte Carlo simulations when periodic boundary condition and Ewald summation methods are used. Another challenge is that constant excess chemical potential GCMC simulations for charged solutes suffer from inadequate insertion and deletion acceptance ratios. In this work, we address those problems by implementing an oscillating excess chemical potential GCMC algorithm with smooth particle mesh Ewald and finite-box-size corrections to treat the long-range electrostatics. The developed GCMC simulation program was combined with GROMACS to perform GCMC/MD simulations of ionic solutions individually containing Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, I-, Ca2+, and Mg2+, respectively. Our simulation results show that the combined GCMC/MD approach can approximate the ionic hydration free energies with proper treatment of long-range electrostatics. Our developed simulation approach can open up new avenues for simulating complex chemical and biomolecular systems and for drug discovery.
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Affiliation(s)
- Delin Sun
- Department of Pharmaceutical Sciences, School of Pharmacy , University of Maryland , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | | | - Sunhwan Jo
- SilcsBio LLC , 8 Market Place , Suite 300, Baltimore , Maryland 21202 , United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy , University of Maryland , 20 Penn Street , Baltimore , Maryland 21201 , United States.,SilcsBio LLC , 8 Market Place , Suite 300, Baltimore , Maryland 21202 , United States
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44
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Ross GA, Bruce Macdonald HE, Cave-Ayland C, Cabedo Martinez AI, Essex JW. Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo. J Chem Theory Comput 2017; 13:6373-6381. [PMID: 29091438 PMCID: PMC5729546 DOI: 10.1021/acs.jctc.7b00738] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
The
ability of grand canonical Monte Carlo (GCMC) to create and
annihilate molecules in a given region greatly aids the identification
of water sites and water binding free energies in protein cavities.
However, acceptance rates without the application of biased moves
can be low, resulting in large variations in the observed water occupancies.
Here, we show that replica-exchange of the chemical potential significantly
reduces the variance of the GCMC data. This improvement comes at a
negligible increase in computational expense when simulations comprise
of runs at different chemical potentials. Replica-exchange GCMC is
also found to substantially increase the precision of water binding
free energies as calculated with grand canonical integration, which
has allowed us to address a missing standard state correction.
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Affiliation(s)
- Gregory A Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | | | | | - Ana I Cabedo Martinez
- Department of Chemistry, University of Southampton , Southampton, SO17 1BJ, United Kingdom
| | - Jonathan W Essex
- Department of Chemistry, University of Southampton , Southampton, SO17 1BJ, United Kingdom
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45
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Gioia D, Bertazzo M, Recanatini M, Masetti M, Cavalli A. Dynamic Docking: A Paradigm Shift in Computational Drug Discovery. Molecules 2017; 22:molecules22112029. [PMID: 29165360 PMCID: PMC6150405 DOI: 10.3390/molecules22112029] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
Molecular docking is the methodology of choice for studying in silico protein-ligand binding and for prioritizing compounds to discover new lead candidates. Traditional docking simulations suffer from major limitations, mostly related to the static or semi-flexible treatment of ligands and targets. They also neglect solvation and entropic effects, which strongly limits their predictive power. During the last decade, methods based on full atomistic molecular dynamics (MD) have emerged as a valid alternative for simulating macromolecular complexes. In principle, compared to traditional docking, MD allows the full exploration of drug-target recognition and binding from both the mechanistic and energetic points of view (dynamic docking). Binding and unbinding kinetic constants can also be determined. While dynamic docking is still too computationally expensive to be routinely used in fast-paced drug discovery programs, the advent of faster computing architectures and advanced simulation methodologies are changing this scenario. It is feasible that dynamic docking will replace static docking approaches in the near future, leading to a major paradigm shift in in silico drug discovery. Against this background, we review the key achievements that have paved the way for this progress.
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Affiliation(s)
- Dario Gioia
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
| | - Martina Bertazzo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Maurizio Recanatini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
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46
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Raman EP, Lakkaraju SK, Denny RA, MacKerell AD. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. J Comput Chem 2017; 38:1238-1251. [PMID: 27782307 PMCID: PMC5403604 DOI: 10.1002/jcc.24522] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022]
Abstract
Accurate and rapid estimation of relative binding affinities of ligand-protein complexes is a requirement of computational methods for their effective use in rational ligand design. Of the approaches commonly used, free energy perturbation (FEP) methods are considered one of the most accurate, although they require significant computational resources. Accordingly, it is desirable to have alternative methods of similar accuracy but greater computational efficiency to facilitate ligand design. In the present study relative free energies of binding are estimated for one or two non-hydrogen atom changes in compounds targeting the proteins ACK1 and p38 MAP kinase using three methods. The methods include standard FEP, single-step free energy perturbation (SSFEP) and the site-identification by ligand competitive saturation (SILCS) ligand grid free energy (LGFE) approach. Results show the SSFEP and SILCS LGFE methods to be competitive with or better than the FEP results for the studied systems, with SILCS LGFE giving the best agreement with experimental results. This is supported by additional comparisons with published FEP data on p38 MAP kinase inhibitors. While both the SSFEP and SILCS LGFE approaches require a significant upfront computational investment, they offer a 1000-fold computational savings over FEP for calculating the relative affinities of ligand modifications once those pre-computations are complete. An illustrative example of the potential application of these methods in the context of screening large numbers of transformations is presented. Thus, the SSFEP and SILCS LGFE approaches represent viable alternatives for actively driving ligand design during drug discovery and development. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- E. Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | - Sirish Kaushik Lakkaraju
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | - Rajiah Aldrin Denny
- Medicine Design, Worldwide Research & Development, Pfizer Inc, 610 Main Street, Cambridge, MA 02139, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
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47
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Arcon JP, Defelipe LA, Modenutti CP, López ED, Alvarez-Garcia D, Barril X, Turjanski AG, Martí MA. Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. J Chem Inf Model 2017; 57:846-863. [DOI: 10.1021/acs.jcim.6b00678] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan Pablo Arcon
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Lucas A. Defelipe
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Carlos P. Modenutti
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Elias D. López
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | | | - Xavier Barril
- Institut
de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat
de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Adrián G. Turjanski
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
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Abstract
Computational approaches are useful tools to interpret and guide experiments to expedite the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) are the two general types of computer-aided drug design (CADD) approaches in existence. SBDD methods analyze macromolecular target 3-dimensional structural information, typically of proteins or RNA, to identify key sites and interactions that are important for their respective biological functions. Such information can then be utilized to design antibiotic drugs that can compete with essential interactions involving the target and thus interrupt the biological pathways essential for survival of the microorganism(s). LBDD methods focus on known antibiotic ligands for a target to establish a relationship between their physiochemical properties and antibiotic activities, referred to as a structure-activity relationship (SAR), information that can be used for optimization of known drugs or guide the design of new drugs with improved activity. In this chapter, standard CADD protocols for both SBDD and LBDD will be presented with a special focus on methodologies and targets routinely studied in our laboratory for antibiotic drug discoveries.
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Lemkul J, Lakkaraju SK, MacKerell AD. Characterization of Mg 2+ Distributions around RNA in Solution. ACS OMEGA 2016; 1:680-688. [PMID: 27819065 PMCID: PMC5088455 DOI: 10.1021/acsomega.6b00241] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 10/17/2016] [Indexed: 05/20/2023]
Abstract
Binding of metal ions is an important factor governing the folding and dynamics of RNA. Shielding of charges in the polyanionic backbone allows RNA to adopt a diverse range of folded structures that give rise to their many functions within the cell. Some RNA sequences fold only in the presence of Mg2+, which may be bound via direct interactions or occupy the more diffuse "ion atmosphere" around the RNA. To understand the driving forces for RNA folding, it is important to be able to fully characterize the distribution of metal ions around the RNA. In this work, a combined Grand Canonical Monte Carlo-Molecular Dynamics (GCMC-MD) method is applied to characterize Mg2+ distributions around folded RNA structures. The GCMC-MD approach identifies known inner- and outer-shell Mg2+ coordination, while also predicting new regions occupied by Mg2+ that are not observed in crystal structures but that may be relevant in solution, including the case of the Mg2+ riboswitch, for which alternate Mg2+ binding sites may have implications for its function. This work represents a significant step forward in establishing a structural and thermodynamic description of RNA-Mg2+ interactions and their role in RNA structure and function.
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50
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Ghanakota P, Carlson HA. Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics. J Med Chem 2016; 59:10383-10399. [PMID: 27486927 DOI: 10.1021/acs.jmedchem.6b00399] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Identifying binding hotspots on protein surfaces is of prime interest in structure-based drug discovery, either to assess the tractability of pursuing a protein target or to drive improved potency of lead compounds. Computational approaches to detect such regions have traditionally relied on energy minimization of probe molecules onto static protein conformations in the absence of the natural aqueous environment. Advances in high performance computing now allow us to assess hotspots using molecular dynamics (MD) simulations. MD simulations integrate protein flexibility and the complicated role of water, thereby providing a more realistic assessment of the complex kinetics and thermodynamics at play. In this review, we describe the evolution of various cosolvent-based MD techniques and highlight a myriad of potential applications for such technologies in computational drug development.
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Affiliation(s)
- Phani Ghanakota
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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