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Article ; Online: GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.

Zhao, Mingtian / Kognole, Abhishek A / Jo, Sunhwan / Tao, Aoxiang / Hazel, Anthony / MacKerell, Alexander D

2023 Volume 44, Issue 20, Page(s) 1719–1732

Abstract: The Grand Canonical Monte Carlo (GCMC) ensemble defined by the excess chemical potential, ... ...

Abstract	The Grand Canonical Monte Carlo (GCMC) ensemble defined by the excess chemical potential, μ
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.27121
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Article ; Online: Structural and thermodynamic framework for PIEZO1 modulation by small molecules.

Jiang, Wenjuan / Wijerathne, Tharaka D / Zhang, Han / Lin, Yi-Chun / Jo, Sunhwan / Im, Wonpil / Lacroix, Jerome J / Luo, Yun L

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 50, Page(s) e2310933120

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 ... ...

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.
MeSH term(s)	Ion Channels/metabolism ; High-Throughput Screening Assays ; Drug Discovery ; Binding Sites ; Thermodynamics ; Mechanotransduction, Cellular/physiology
Chemical Substances	Ion Channels
Language	English
Publishing date	2023-12-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2310933120
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Article: Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.

Goel, Himanshu / Hazel, Anthony / Yu, Wenbo / Jo, Sunhwan / MacKerell, Alexander D

New journal of chemistry = Nouveau journal de chimie

2021 Volume 46, Issue 3, Page(s) 919–932

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 ... ...

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.
Language	English
Publishing date	2021-11-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1472933-7
ISSN	1369-9261 ; 1144-0546
ISSN (online)	1369-9261
ISSN	1144-0546
DOI	10.1039/d1nj04028f
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Article: Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation.

Goel, Himanshu / Hazel, Anthony / Ustach, Vincent D / Jo, Sunhwan / Yu, Wenbo / MacKerell, Alexander D

Chemical science

2021 Volume 12, Issue 25, Page(s) 8844–8858

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 ... ...

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
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d1sc01781k
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Article: Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

Jiang, Wei / Thirman, Jonathan / Jo, Sunhwan / Roux, Benoît

Journal of physical chemistry. 2018 Sept. 25, v. 122, no. 41

2018

Abstract: Replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free-energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD ... ...

Abstract	Replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free-energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559–2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a preidentified “solute” and a second one via the introduction of flattening torsional free-energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of p-xylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. The tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free-energy computations.
Keywords	Gibbs free energy ; algorithms ; ligands ; lysozyme ; molecular dynamics ; mutants ; potential energy ; tempering ; xylene
Language	English
Dates of publication	2018-0925
Size	p. 9435-9442.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.8b03277
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Article ; Online: Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.

Jiang, Wei / Thirman, Jonathan / Jo, Sunhwan / Roux, Benoît

The journal of physical chemistry. B

2018 Volume 122, Issue 41, Page(s) 9435–9442

Abstract	Replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free-energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a preidentified "solute" and a second one via the introduction of flattening torsional free-energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of p-xylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. The tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free-energy computations.
MeSH term(s)	Algorithms ; Bacteriophage T4/enzymology ; Benzene Derivatives/chemistry ; Benzene Derivatives/metabolism ; Binding Sites ; Molecular Dynamics Simulation ; Muramidase/chemistry ; Muramidase/metabolism ; Protein Binding ; Quantum Theory ; Thermodynamics ; Xylenes/chemistry ; Xylenes/metabolism
Chemical Substances	Benzene Derivatives ; Xylenes ; 4-xylene (6WAC1O477V) ; Muramidase (EC 3.2.1.17) ; n-butylbenzene (S8XZ2901RZ)
Language	English
Publishing date	2018-10-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.8b03277
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Article: Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots)

MacKerell, Alexander D / Jo, Sunhwan / Lakkaraju, Sirish Kaushik / Lind, Christoffer / Yu, Wenbo

Biochimica et biophysica acta. 2020 Apr., v. 1864, no. 4

2020

Abstract: 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 ... ...

Abstract	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.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.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.The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
Keywords	G-protein coupled receptors ; androgen receptors ; binding capacity ; binding sites ; cyclin-dependent kinase ; fatty acids ; ligands
Language	English
Dates of publication	2020-04
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2020.129519
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Article ; Online: String Method for Protein-Protein Binding Free-Energy Calculations.

Suh, Donghyuk / Jo, Sunhwan / Jiang, Wei / Chipot, Chris / Roux, Benoît

Journal of chemical theory and computation

2019 Volume 15, Issue 11, Page(s) 5829–5844

Abstract: A powerful computational strategy to determine the equilibrium association constant of two macromolecules with explicit-solvent molecular dynamics (MD) simulations is the "geometric route", which considers the reversible physical separation of the bound ... ...

Abstract	A powerful computational strategy to determine the equilibrium association constant of two macromolecules with explicit-solvent molecular dynamics (MD) simulations is the "geometric route", which considers the reversible physical separation of the bound complex in solution. Nonetheless, multiple challenges remain to render this type of methodology reliable and computationally efficient in practice. In particular, in one, formulation of the geometric route relies on the potential of mean force (PMF) for physically separating the two binding partners restrained along a straight axis, which must be selected prior to the calculation. However, practical applications indicate that the calculation of the separation PMF along the predefined rectilinear pathway may be suboptimal and slowly convergent. Recognizing that a rectilinear straight separation pathway is generally not representative of how the protein complex physically separates in solution, we put forth a novel theoretical framework for binding free-energy calculations, leaning on the optimal curvilinear minimum free-energy path (MFEP) determined from the string method. The proposed formalism is validated by comparing the results obtained using both rectilinear and curvilinear pathways for a prototypical host-guest complex formed by cucurbit[7]uril (CB[7]) binding benzene, and for the barnase-barstar protein complex. On the basis of multi-microsecond MD calculations, we find that the calculations following the traditional rectilinear pathway and the string-based curvilinear pathway agree quantitatively, but convergence is faster with the latter.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Benzene/chemistry ; Benzene/metabolism ; Bridged-Ring Compounds/chemistry ; Bridged-Ring Compounds/metabolism ; Imidazoles/chemistry ; Imidazoles/metabolism ; Molecular Dynamics Simulation ; Protein Binding ; Proteins/chemistry ; Proteins/metabolism ; Ribonucleases/chemistry ; Ribonucleases/metabolism ; Thermodynamics
Chemical Substances	Bacterial Proteins ; Bridged-Ring Compounds ; Imidazoles ; Proteins ; cucurbit(7)uril ; barstar protein, Bacillus amyloliquefaciens (37328-61-3) ; Ribonucleases (EC 3.1.-) ; Bacillus amyloliquefaciens ribonuclease (EC 3.1.27.-) ; Benzene (J64922108F)
Language	English
Publishing date	2019-10-31
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.9b00499
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Article ; Online: Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection Using the Site Identification by Ligand Competitive Saturation-Biologics Approach.

Jo, Sunhwan / Xu, Amy / Curtis, Joseph E / Somani, Sandeep / MacKerell, Alexander D

Molecular pharmaceutics

2020 Volume 17, Issue 11, Page(s) 4323–4333

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 ... ...

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
MeSH term(s)	Antibodies, Monoclonal/chemistry ; Arginine/chemistry ; Binding Sites ; Biological Products/chemistry ; Drug Compounding/methods ; Excipients/chemistry ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin G/chemistry ; Kinetics ; Ligands ; Molecular Docking Simulation/methods ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Stability ; Sucrose/chemistry ; Trehalose/chemistry ; Viscosity
Chemical Substances	Antibodies, Monoclonal ; Biological Products ; Excipients ; Immunoglobulin Fab Fragments ; Immunoglobulin G ; Ligands ; Sucrose (57-50-1) ; Arginine (94ZLA3W45F) ; Trehalose (B8WCK70T7I)
Language	English
Publishing date	2020-10-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2138405-8
ISSN	1543-8392 ; 1543-8384
ISSN (online)	1543-8392
ISSN	1543-8384
DOI	10.1021/acs.molpharmaceut.0c00775
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Zs.A 6250: Show issues

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Article ; Online: Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots).

MacKerell, Alexander D / Jo, Sunhwan / Lakkaraju, Sirish Kaushik / Lind, Christoffer / Yu, Wenbo

Biochimica et biophysica acta. General subjects

2020 Volume 1864, Issue 4, Page(s) 129519

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 ... ...

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.
MeSH term(s)	Allosteric Site ; Binding Sites/drug effects ; Cyclin-Dependent Kinase 5/antagonists & inhibitors ; Humans ; Ligands ; Mitogen-Activated Protein Kinase 7/antagonists & inhibitors ; Molecular Docking Simulation ; Protein Tyrosine Phosphatases/antagonists & inhibitors ; Receptor, Muscarinic M2/antagonists & inhibitors ; Receptors, Adrenergic, beta-2/metabolism ; Receptors, Androgen/metabolism ; Receptors, G-Protein-Coupled/antagonists & inhibitors
Chemical Substances	FFAR1 protein, human ; Ligands ; Receptor, Muscarinic M2 ; Receptors, Adrenergic, beta-2 ; Receptors, Androgen ; Receptors, G-Protein-Coupled ; Cyclin-Dependent Kinase 5 (EC 2.7.11.1) ; MAPK7 protein, human (EC 2.7.11.24) ; Mitogen-Activated Protein Kinase 7 (EC 2.7.11.24) ; Protein Tyrosine Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2020-01-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagen.2020.129519
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