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Article ; Online: FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design.

Perez, Carles / Soler, Daniel / Soliva, Robert / Guallar, Victor

Journal of chemical information and modeling

2020 Volume 60, Issue 3, Page(s) 1728–1736

Abstract: The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, requiring multiple iterations of ... ...

Abstract	The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, requiring multiple iterations of trial and error designs, an ideal scenario for applying computer simulation. However, most state-of-the-art modeling techniques fail to provide a fast and reliable answer to the Induced-Fit protein-ligand problem. To aid in this matter, we present FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a fragment from a bound core while exploring the protein-ligand conformational space. We tested the ability of FragPELE to predict crystallographic data, even in cases where cryptic sub-pockets open because of the presence of particular R-groups. Additionally, we evaluated the potential of the software on growing and scoring five congeneric series from the 2015 FEP+ dataset, comparing them to FEP+, SP and Induced-Fit Glide, and MMGBSA simulations. Results show that FragPELE could be useful not only for finding new cavities and novel binding modes in cases where standard docking tools cannot but also to rank ligand activities in a reasonable amount of time and with acceptable precision.
MeSH term(s)	Binding Sites ; Computer Simulation ; Drug Design ; Ligands ; Molecular Docking Simulation ; Protein Binding ; Software
Chemical Substances	Ligands
Language	English
Publishing date	2020-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.9b00938
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Article ; Online: Extensive benchmark of rDock as a peptide-protein docking tool.

Soler, Daniel / Westermaier, Yvonne / Soliva, Robert

Journal of computer-aided molecular design

2019 Volume 33, Issue 7, Page(s) 613–626

Abstract: Peptide-protein interactions are ubiquitous in living cells and essential to a wide range of biological processes, as well as pathologies such as cancer or cardiovascular disease. Yet, obtaining reliable binding mode predictions in peptide-protein ... ...

Abstract	Peptide-protein interactions are ubiquitous in living cells and essential to a wide range of biological processes, as well as pathologies such as cancer or cardiovascular disease. Yet, obtaining reliable binding mode predictions in peptide-protein docking remains a great challenge for most computational docking programs. The main goal of this study was to assess the performance of the small molecule docking program rDock in comparison to other widely used small molecule docking programs, using 100 peptide-protein systems with peptides ranging from 2 to 12 residues. As we used two large independent benchmark sets previously published for other small-molecule docking programs (AutoDockVina benchmark and LEADSPEP), the performance of rDock could directly be compared to the performances of AutoDockVina, Surflex, GOLD, and Glide, as well as to the peptide docking protocol PIPER-FlexPepDock and the webserver HPepDock. Our benchmark reveals that rDock can dock the 100 peptides with an overall backbone RMSD below 2.5 Å in 58.5% of the cases (76% for the 47 systems of the AutoDockVina benchmark set and 43% for the 53 systems of the LEADSPEP benchmark set). More specifically, rDock docks up to 11-residue peptides with a backbone RMSD below 2.5 Å in 60.75% of the cases. rDock displays higher accuracy than most available small molecule docking programs for 6-10-residue peptides and can sometimes perform similarly to the peptide docking tool, especially at a high level of exhaustiveness (100 or 150 runs). Its performance, as is the case for many other unguided small molecule docking tools, is compromised when the peptides adopt secondary structures upon binding. However, our analyses suggest that rDock could be used for predicting how medium-sized biologically relevant peptides bind to their respective protein targets when the latter bind in an extended mode.
MeSH term(s)	Databases, Protein ; Molecular Docking Simulation ; Peptides/chemistry ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Proteins/chemistry ; Proteins/metabolism ; Software
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2019-07-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-019-00212-0
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Article ; Online: Exploring the Conformational Landscape of Bioactive Small Molecules.

Zivanovic, Sanja / Colizzi, Francesco / Moreno, David / Hospital, Adam / Soliva, Robert / Orozco, Modesto

Journal of chemical theory and computation

2020 Volume 16, Issue 10, Page(s) 6575–6585

Abstract: By using a combination of classical Hamiltonian replica exchange with high-level quantum mechanical calculations on more than one hundred drug-like molecules, we explored here the energy cost associated with binding of drug-like molecules to target ... ...

Abstract	By using a combination of classical Hamiltonian replica exchange with high-level quantum mechanical calculations on more than one hundred drug-like molecules, we explored here the energy cost associated with binding of drug-like molecules to target macromolecules. We found that, in general, the drug-like molecules present bound to proteins in the Protein Data Bank (PDB) can access easily the bioactive conformation and in fact for 73% of the studied molecules the "bioactive" conformation is within 3
MeSH term(s)	Databases, Protein ; Density Functional Theory ; Ligands ; Models, Molecular ; Molecular Conformation ; Molecular Weight ; Proteins/chemistry ; Small Molecule Libraries/chemistry
Chemical Substances	Ligands ; Proteins ; Small Molecule Libraries
Language	English
Publishing date	2020-09-02
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.0c00304
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Article ; Online: DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs.

Moreno, David / Zivanovic, Sanja / Colizzi, Francesco / Hospital, Adam / Aranda, Juan / Soliva, Robert / Orozco, Modesto

Journal of chemical theory and computation

2020 Volume 16, Issue 10, Page(s) 6598–6608

Abstract: We present drug force-field recalibration (DFFR), a new method for refining of automatic force-fields used to represent small drugs in docking and molecular dynamics simulations. The method is based on fine-tuning of torsional terms to obtain ensembles ... ...

Abstract	We present drug force-field recalibration (DFFR), a new method for refining of automatic force-fields used to represent small drugs in docking and molecular dynamics simulations. The method is based on fine-tuning of torsional terms to obtain ensembles that reproduce observables derived from reference data. DFFR is fast and flexible and can be easily automatized for a high-throughput regime, making it useful in drug-design projects. We tested the performance of the method in a few model systems and also in a variety of druglike molecules using reference data derived from: (i) density functional theory coupled to a self-consistent reaction field (DFT/SCRF) calculations on highly populated conformers and (ii) enhanced sampling quantum mechanical/molecular mechanics (QM/MM) where the drug is reproduced at the QM level, while the solvent is represented by classical force-fields. Extension of the method to include other sources of reference data is discussed.
MeSH term(s)	Automation ; Calibration ; Density Functional Theory ; High-Throughput Screening Assays ; Molecular Dynamics Simulation ; Pharmaceutical Preparations/chemistry
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2020-09-29
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.0c00306
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Article: Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose

Díaz, Lucía / Soler, Daniel / Tresadern, Gary / Buyck, Christophe / Perez-Benito, Laura / Saen-Oon, Suwipa / Guallar, Victor / Soliva, Robert

RSC advances. 2020 Feb. 17, v. 10, no. 12

2020

Abstract: In silico binding site location and pose prediction for a molecule targeted at a large protein surface is a challenging task. We report a blind test with two peptidomimetic molecules that bind the flu virus hemagglutinin (HA) surface antigen, JNJ7918 and ...

Abstract	In silico binding site location and pose prediction for a molecule targeted at a large protein surface is a challenging task. We report a blind test with two peptidomimetic molecules that bind the flu virus hemagglutinin (HA) surface antigen, JNJ7918 and JNJ4796 (recently disclosed in van Dongen et al., Science, 2019, 363). Tests with a series of conventional approaches such as rigid (receptor) docking against available X-ray crystal structures or against an ensemble of structures generated by quick methodologies (NMA, homology modeling) gave mixed results, due to the shallowness and flexibility of the binding site and the sheer size of the target. However, tests with our Monte Carlo platform PELE in two protocols involving either exploration of the whole protein surface (global exploration), or the latter followed by refinement of best solutions (local exploration) yielded remarkably good results by locating the actual binding site and generating binding modes that recovered all native contacts found in the X-ray structures. Thus, the Monte Carlo scheme of PELE seems promising as a quick methodology to overcome the challenge of identifying entirely unknown binding sites and modes for protein–protein disruptors.
Keywords	Monte Carlo method ; Orthomyxoviridae ; X-radiation ; binding sites ; computer simulation ; crystal structure ; hemagglutinins ; models ; prediction ; surface antigens
Language	English
Dates of publication	2020-0217
Size	p. 7058-7064.
Publishing place	The Royal Society of Chemistry
Document type	Article
ISSN	2046-2069
DOI	10.1039/d0ra01127d
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca

Kotev, Martin / Pascual, Rosalia / Almansa, Carmen / Guallar, Victor / Soliva, Robert

Journal of chemical information and modeling

2018 Volume 58, Issue 8, Page(s) 1707–1715

Abstract: Cryo-electron microscopy (cryo-EM) is emerging as a real alternative for structural elucidation. In spite of this, very few cryo-EM structures have been described so far as successful platforms for in silico drug design. Gabapentin and pregabalin are ... ...

Abstract	Cryo-electron microscopy (cryo-EM) is emerging as a real alternative for structural elucidation. In spite of this, very few cryo-EM structures have been described so far as successful platforms for in silico drug design. Gabapentin and pregabalin are some of the most successful drugs in the treatment of epilepsy and neuropathic pain. Although both are in clinical use and are known to exert their effects by binding to the regulatory α2δ subunit of voltage gated calcium channels, their binding modes have never been characterized. We describe here the successful use of an exhaustive protein-ligand sampling algorithm on the α2δ-1 subunit of the recently published cryo-EM structure, with the goal of characterizing the ligand entry path and binding mode for gabapentin, pregabalin, and several other amino acidic α2δ-1 ligands. Our studies indicate that (i) all simulated drugs explore the same path for accessing the occluded binding site on the interior of the α2δ-1 subunit; (ii) they all roughly occupy the same pocket; (iii) the plasticity of the binding site allows the accommodation of a variety of amino acidic modulators, driven by the flexible "capping loop" delineated by residues Tyr426-Val435 and the floppy nature of Arg217; (iv) the predicted binding modes are in line with previously available mutagenesis data, confirming Arg217 as key for binding, with Asp428 and Asp467 highlighted as additional anchoring points for all amino acidic drugs. The study is one of the first proofs that latest-generation cryo-EM structures combined with exhaustive computational methods can be exploited in early drug discovery.
MeSH term(s)	Algorithms ; Analgesics/chemistry ; Analgesics/pharmacology ; Binding Sites ; Calcium Channels/chemistry ; Calcium Channels/metabolism ; Calcium Channels/ultrastructure ; Cryoelectron Microscopy ; Gabapentin/chemistry ; Gabapentin/pharmacology ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pregabalin/chemistry ; Pregabalin/pharmacology ; Protein Binding
Chemical Substances	Analgesics ; CACNA2D1 protein, human ; Calcium Channels ; Ligands ; Pregabalin (55JG375S6M) ; Gabapentin (6CW7F3G59X)
Language	English
Publishing date	2018-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.8b00347
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Article ; Online: Challenges of docking in large, flexible and promiscuous binding sites.

Kotev, Martin / Soliva, Robert / Orozco, Modesto

Bioorganic & medicinal chemistry

2016 Volume 24, Issue 20, Page(s) 4961–4969

Abstract: After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; (ii) the flexibility of both ... ...

Abstract	After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; (ii) the flexibility of both interacting partners, and (iii) the differential solvation of bound and unbound partners. We have evaluated the performance of standard rigid(receptor)/flexible(ligand) docking approaches with respect to last-generation fully flexible docking methods to obtain reasonable poses in a very challenging case: soluble Epoxide Hydrolase (sEH), a flexible protein showing different binding sites. We found that full description of the flexibility of both protein and ligand and accurate description of solvation leads to significant improvement in the ability of docking to reproduce well known binding modes, and at the same time capture the intrinsic binding promiscuity of the protein.
MeSH term(s)	Binding Sites ; Epoxide Hydrolases/antagonists & inhibitors ; Epoxide Hydrolases/chemistry ; Epoxide Hydrolases/metabolism ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Structure ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology
Chemical Substances	Ligands ; Small Molecule Libraries ; Epoxide Hydrolases (EC 3.3.2.-)
Language	English
Publishing date	2016-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2016.08.010
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Article ; Online: Atomistic simulations shed new light on the activation mechanisms of RORγ and classify it as Type III nuclear hormone receptor regarding ligand-binding paths.

Saen-Oon, Suwipa / Lozoya, Estrella / Segarra, Victor / Guallar, Victor / Soliva, Robert

Scientific reports

2019 Volume 9, Issue 1, Page(s) 17249

Abstract: The molecular recognition of the RORγ nuclear hormone receptor (NHR) ligand-binding domain (LBD) has been extensively studied with numerous X-ray crystal structures. However, the picture afforded by these complexes is static and does not fully explain ... ...

Abstract	The molecular recognition of the RORγ nuclear hormone receptor (NHR) ligand-binding domain (LBD) has been extensively studied with numerous X-ray crystal structures. However, the picture afforded by these complexes is static and does not fully explain the functional behavior of the LBD. In particular, the apo structure of the LBD seems to be in a fully active state, with no obvious differences to the agonist-bound structure. Further, several atypical in vivo inverse agonists have surprisingly been found to co-crystallize with the LBD in agonist mode (with co-activator), leading to a disconnection between molecular recognition and functional activity. Moreover, the experimental structures give no clues on how RORγ LBD binders access the interior of the LBD. To address all these points, we probe here, with a variety of simulation techniques, the fine structural balance of the RORγ LBD in its apo vs. holo form, the differences in flexibility and stability of the LBD in complex with agonists vs. inverse agonists and how binders diffuse in and out of the LBD in unbiased simulations. Our data conclusively point to the stability afforded by the so-called "agonist lock" between H479 and Y502 and the precise location of Helix 12 (H12) for the competence of the LBD to bind co-activator proteins. We observe the "water trapping" mechanism suggested previously for the atypical inverse agonists and discover a different behavior for the latter when co-activator is present or absent, which might help explain their conflicting data. Additionally, we unveil the same entry/exit path for agonists and inverse agonist into and out of the LBD for RORγ, suggesting it belongs to the type III NHR sub-family.
MeSH term(s)	Binding Sites/physiology ; Humans ; Ligands ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Protein Binding/physiology ; Protein Conformation ; Receptors, Cytoplasmic and Nuclear/metabolism
Chemical Substances	Ligands ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Receptors, Cytoplasmic and Nuclear
Language	English
Publishing date	2019-11-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-52319-x
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Article ; Online: High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations.

Suriñach, Aristarc / Hospital, Adam / Westermaier, Yvonne / Jordà, Luis / Orozco-Ruiz, Sergi / Beltrán, Daniel / Colizzi, Francesco / Andrio, Pau / Soliva, Robert / Municoy, Martí / Gelpí, Josep Lluís / Orozco, Modesto

Journal of chemical information and modeling

2022 Volume 63, Issue 1, Page(s) 321–334

Abstract: Mutations in the kinase domain of the epidermal growth factor receptor (EGFR) can be drivers of cancer and also trigger drug resistance in patients receiving chemotherapy treatment based on kinase inhibitors. ...

Abstract	Mutations in the kinase domain of the epidermal growth factor receptor (EGFR) can be drivers of cancer and also trigger drug resistance in patients receiving chemotherapy treatment based on kinase inhibitors.
MeSH term(s)	Humans ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Lung Neoplasms/drug therapy ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/chemistry ; Drug Resistance/genetics ; ErbB Receptors/metabolism ; Mutation ; Drug Resistance, Neoplasm/genetics
Chemical Substances	Protein Kinase Inhibitors ; ErbB Receptors (EC 2.7.10.1)
Language	English
Publishing date	2022-12-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.2c01344
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Article ; Online: Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up

Zivanovic, Sanja / Bayarri, Genís / Colizzi, Francesco / Moreno, David / Gelpí, Josep Lluís / Soliva, Robert / Hospital, Adam / Orozco, Modesto

Journal of chemical theory and computation

2020 Volume 16, Issue 10, Page(s) 6586–6597

Abstract: Modern high-throughput structure-based drug discovery algorithms consider ligand flexibility, but typically with low accuracy, which results in a loss of performance in the derived models. Here we present the bioactive conformational ensemble (BCE) ... ...

Abstract	Modern high-throughput structure-based drug discovery algorithms consider ligand flexibility, but typically with low accuracy, which results in a loss of performance in the derived models. Here we present the bioactive conformational ensemble (BCE) server and its associated database. The server creates conformational ensembles of drug-like ligands and stores them in the BCE database, where a variety of analyses are offered to the user. The workflow implemented in the BCE server combines enhanced sampling molecular dynamics with self-consistent reaction field quantum mechanics (SCRF/QM) calculations. The server automatizes all of the steps to transform one-dimensional (1D) or 2D representation of drugs into 3D molecules, which are then titrated, parametrized, hydrated, and optimized before being subjected to Hamiltonian replica-exchange (HREX) molecular dynamics simulations. Ensembles are collected and subjected to a clustering procedure to derive representative conformers, which are then analyzed at the SCRF/QM level of theory. All structural data are organized in a noSQL database accessible through a graphical interface and in a programmatic manner through a REST API. The server allows the user to define a private workspace and offers a deposition protocol as well as input files for "in house" calculations in those cases where confidentiality is a must. The database and the associated server are available at https://mmb.irbbarcelona.org/BCE.
MeSH term(s)	Databases, Factual ; Drug Discovery ; High-Throughput Screening Assays ; Molecular Conformation ; Molecular Dynamics Simulation ; Pharmaceutical Preparations/chemistry ; Quantum Theory
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2020-09-01
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.0c00305
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