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Article: The role of loop dynamics in the prediction of ligand-protein binding enthalpy.

Çınaroğlu, Süleyman Selim / Biggin, Philip C

2023 Volume 14, Issue 24, Page(s) 6792–6805

Abstract: The enthalpic and entropic components of ligand-protein binding free energy reflect the interactions and dynamics between ligand and protein. Despite decades of study, our understanding and hence our ability to predict these individual components remains ...

Abstract	The enthalpic and entropic components of ligand-protein binding free energy reflect the interactions and dynamics between ligand and protein. Despite decades of study, our understanding and hence our ability to predict these individual components remains poor. In recent years, there has been substantial effort and success in the prediction of relative and absolute binding free energies, but the prediction of the enthalpic (and entropic) contributions in biomolecular systems remains challenging. Indeed, it is not even clear what kind of performance in terms of accuracy could currently be obtained for such systems. It is, however, relatively straight-forward to compute the enthalpy of binding. We thus evaluated the performance of absolute enthalpy of binding calculations using molecular dynamics simulation for ten inhibitors against a member of the bromodomain family, BRD4-1, against isothermal titration calorimetry data. Initial calculations, with the AMBER force-field showed good agreement with experiment (
Language	English
Publishing date	2023-06-01
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/d2sc06471e
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Article ; Online: Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems.

Çınaroğlu, Süleyman Selim / Biggin, Philip C

Journal of chemical information and modeling

2023 Volume 63, Issue 19, Page(s) 6095–6108

Abstract: Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt ...

Abstract	Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt to directly compute the enthalpic contribution to binding. Indeed, the prevailing assumption has been that the errors associated with such approaches would be too large for them to be meaningful. Nevertheless, we currently have no indication of how well the present methods would perform in terms of predicting the enthalpy of binding for protein-peptide complexes. To that end, we carefully assembled and curated a set of 11 protein-peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding. The initial "out of the box" calculations were, as expected, very modest in terms of agreement with the experiment. However, careful inspection of the outliers allows for the identification of key sampling problems such as distinct conformations of peptide termini not being sampled or suboptimal cofactor parameters. Additional simulations guided by these aspects can lead to a respectable correlation with isothermal titration calorimetry (ITC) experiments (
MeSH term(s)	Proteins/chemistry ; Thermodynamics ; Peptides/chemistry ; Calorimetry/methods ; Protein Binding
Chemical Substances	Proteins ; Peptides
Language	English
Publishing date	2023-09-27
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.3c01041
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Article ; Online: Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems.

Çınaroğlu, Süleyman Selim / Biggin, Philip C

The journal of physical chemistry. B

2021 Volume 125, Issue 6, Page(s) 1558–1567

Abstract: Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the ... ...

Abstract	Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.
Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c11383
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Article ; Online: Computational completion of the Aurora interaction region of N-Myc in the Aurora a kinase complex.

Altiner, Pinar / Çınaroğlu, Süleyman Selim / Timucin, Ahmet Can / Timucin, Emel

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18399

Abstract: Inhibiting protein-protein interactions of the Myc family is a viable pharmacological strategy for modulation of the levels of Myc oncoproteins in cancer. Aurora A kinase (AurA) and N-Myc interaction is one of the most attractive targets of this strategy ...

Abstract	Inhibiting protein-protein interactions of the Myc family is a viable pharmacological strategy for modulation of the levels of Myc oncoproteins in cancer. Aurora A kinase (AurA) and N-Myc interaction is one of the most attractive targets of this strategy because formation of this complex blocks proteasomal degradation of N-Myc in neuroblastoma. Two crystallization studies have captured this complex (PDB IDs: 5g1x, 7ztl), partially resolving the AurA interaction region (AIR) of N-Myc. Prompted by the missing N-Myc fragment in these crystal structures, we modeled the complete structure between AurA and N-Myc, and comprehensively analyzed how the incomplete and complete N-Myc behave in complex by molecular dynamics simulations. Molecular dynamics simulations of the incomplete PDB complex (5g1x) repeatedly showed partial dissociation of the short N-Myc fragment (61-89) from the kinase. The missing N-Myc (19-60) fragment was modeled utilizing the N-terminal lobe of AurA as the protein-protein interaction surface, wherein TPX2, a well-known partner of AurA, also binds. Binding free energy calculations along with flexibility analysis confirmed that the complete AIR of N-Myc stabilizes the complex, accentuating the N-terminal lobe of AurA as a binding site for the missing N-Myc fragment (19-60). We further generated additional models consisting of only the missing N-Myc (19-60), and the fused form of TPX2 (7-43) and N-Myc (61-89). These partners also formed more stable interactions with the N-terminal lobe of AurA than did the incomplete N-Myc fragment (61-89) in the 5g1x complex. Altogether, this study provides structural insights into the involvement of the N-terminus of the AIR of N-Myc and the N-terminal lobe of AurA in formation of a stable complex, reflecting its potential for effective targeting of N-Myc.
MeSH term(s)	Humans ; Aurora Kinase A/chemistry ; Binding Sites ; Epilepsy ; Molecular Dynamics Simulation ; Neuroblastoma ; N-Myc Proto-Oncogene Protein
Chemical Substances	Aurora Kinase A (EC 2.7.11.1) ; MYCN protein, human ; N-Myc Proto-Oncogene Protein ; AURKA protein, human (EC 2.7.11.1)
Language	English
Publishing date	2023-10-26
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/s41598-023-45272-3
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Article ; Online: Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined.

Çınaroğlu, Süleyman Selim / Timuçin, Emel

Journal of chemical information and modeling

2019 Volume 59, Issue 9, Page(s) 3846–3859

Abstract: Extensive usage of molecular docking for computer-aided drug discovery resulted in development of numerous programs with versatile scoring and posing algorithms. Selection of the docking program among these vast number of options is central to the ... ...

Abstract	Extensive usage of molecular docking for computer-aided drug discovery resulted in development of numerous programs with versatile scoring and posing algorithms. Selection of the docking program among these vast number of options is central to the outcome of drug discovery. To this end, comparative assessment studies of docking offer valuable insights into the selection of the optimal tool. Despite the availability of various docking assessment studies, the performance difference of docking programs has not been well addressed on metalloproteins which comprise a substantial portion of the human proteome and have been increasingly targeted for treatment of a wide variety of diseases. This study reports comparative assessment of seven docking programs on a diverse metalloprotein set which was compiled for this study. The refined set of the PDBbind (2017) was screened to gather 710 complexes with metal ion(s) closely located to the ligands (<4 Å). The redundancy was eliminated by clustering and overall 213 complexes were compiled as the nonredundant metalloprotein subset of the PDBbind refined. The scoring, ranking, and posing powers of seven noncommercial docking programs, namely, AutoDock4, AutoDock4
MeSH term(s)	Databases, Protein ; Drug Evaluation, Preclinical ; Ligands ; Metalloproteins/antagonists & inhibitors ; Metalloproteins/chemistry ; Metalloproteins/metabolism ; Molecular Docking Simulation ; Protein Binding ; Protein Conformation
Chemical Substances	Ligands ; Metalloproteins
Language	English
Publishing date	2019-09-10
Publishing country	United States
Document type	Comparative Study ; Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.9b00346
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Article ; Online: Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets.

Çınaroğlu, Süleyman Selim / Timuçin, Emel

Briefings in bioinformatics

2019 Volume 21, Issue 6, Page(s) 2112–2125

Abstract: MM-PB/GBSA methods represent a higher-level scoring theory than docking. This study reports an extensive testing of different MM-GBSA scoring schemes on two bromodomain (BRD) datasets. The first set is composed of 24 BRPF1 complexes, and the second one ... ...

Abstract	MM-PB/GBSA methods represent a higher-level scoring theory than docking. This study reports an extensive testing of different MM-GBSA scoring schemes on two bromodomain (BRD) datasets. The first set is composed of 24 BRPF1 complexes, and the second one is a nonredundant set constructed from the PDBbind and composed of 28 diverse BRD complexes. A variety of MM-GBSA schemes were analyzed to evaluate the performance of four protocols with different numbers of minimization and MD steps, 10 different force fields and three different water models. Results showed that neither additional MD steps nor unfixing the receptor atoms improved scoring or ranking power. On the contrary, our results underscore the advantage of fixing receptor atoms or limiting the number of MD steps not only for a reduction in the computational costs but also for boosting the prediction accuracy. Among Amber force fields tested, ff14SB and its derivatives rather than ff94 or polarized force fields provided the most accurate scoring and ranking results. The TIP3P water model yielded the highest scoring and ranking power compared to the others. Posing power was further evaluated for the BRPF1 set. A slightly better posing power for the protocol which uses both minimization and MD steps with a fixed receptor than the one which uses only minimization with a fully flexible receptor-ligand system was observed. Overall, this study provides insights into the usage of the MM-GBSA methods for screening of BRD inhibitors, substantiating the benefits of shorter protocols and latest force fields and maintaining the crystal waters for accuracy.
MeSH term(s)	Algorithms ; Ligands ; Molecular Dynamics Simulation ; Protein Binding ; Protein Domains ; Research Design
Chemical Substances	Ligands
Language	English
Publishing date	2019-11-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbz143
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Article ; Online: Insights into an alternative benzofuran binding mode and novel scaffolds of polyketide synthase 13 inhibitors.

Çınaroğlu, Süleyman Selim / Timuçin, Emel

Journal of molecular modeling

2019 Volume 25, Issue 5, Page(s) 130

Abstract: Small molecules targeting biosynthesis of mycolic acids in the tuberculosis causing bacterium carry high potential for anti-tuberculosis drug discovery. Hitherto, benzofuran containing molecules were identified to target the thioesterase domain of ... ...

Abstract	Small molecules targeting biosynthesis of mycolic acids in the tuberculosis causing bacterium carry high potential for anti-tuberculosis drug discovery. Hitherto, benzofuran containing molecules were identified to target the thioesterase domain of polyketide synthase 13 (Pks13), one of the crucial constituents of this pathway. Among these, TAM16 was also reported to be highly potent in vivo. Here we performed a multi-stage virtual screening methodology recruiting both ligand- and structure-based screening tools for identification of novel Pks13 inhibitors. The large ZINC15 database comprising more than 1 billion ligands was reduced to 21,277 ligands with benzofuran rings and similarity to TAM16. This collection was screened by docking and the 20 top scoring ligands were further analyzed by molecular dynamics simulations. Molecular mechanics/generalized Born surface area (MM-GBSA) based binding free energy predictions confirmed five molecules in the ZINC15 database lead to remarkable increases in the binding free energy of TAM16. Essentially, the most potent ligand ZINC840169872, which carries a distinct scaffold with a cyclohexane group fused to the furan ring, produced a twofold change in the ligand efficiency of TAM16. Further, assessments of the structure-based tools on five different Pks13-TAM complex structures suggested a high-level agreement with the experiments, substantiating the validity of our methodology for screening Pks13 inhibitors. Overall, these in silico insights into a low energy benzofuran-based scaffold and an alternative binding mode for the benzofuran ring unravel viable strategies to generate potent anti-tuberculosis drugs, accentuating the applications of virtual screening approaches for exploring large compound libraries that cannot be easily accessed by experimentation. Graphical abstract In silico virtual screening of ZINC15 database for the identification of potential inhibitors targeting PKS13.
Language	English
Publishing date	2019-04-25
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-019-4010-y
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Article ; Online: In silico identification of inhibitors targeting N-Terminal domain of human Replication Protein A.

Çınaroğlu, Süleyman Selim / Timuçin, Emel

Journal of molecular graphics & modelling

2018 Volume 86, Page(s) 149–159

Abstract: Replication Protein A (RPA) mediates DNA Damage Response (DDR) pathways through protein-protein interactions (PPIs). Targeting the PPIs formed between RPA and other DNA Damage Response (DDR) mediators has become an intriguing area of research for cancer ... ...

Abstract	Replication Protein A (RPA) mediates DNA Damage Response (DDR) pathways through protein-protein interactions (PPIs). Targeting the PPIs formed between RPA and other DNA Damage Response (DDR) mediators has become an intriguing area of research for cancer drug discovery. A number of studies applied different methods ranging from high throughput screening approaches to fragment-based drug design tools to discover RPA inhibitors. Although these methods are robust, virtual screening approaches may be allocated as an alternative to such experimental methods, especially for screening of large libraries. Here we report the comprehensive screening of the large database, ZINC15 composed of ∼750 M compounds and the comparison of the identified ligands with the previously known inhibitors by means of binding affinity and drug-likeness. Initially, a ligand library sharing similarity with a promising inhibitor of the N-terminal domain of the RPA70 subunit (RPA70N) was generated by screening of the ZINC15 library. 46,999 ligands were collected and screened by LeDock which produced a satisfactory correlation with the experimental values (R
MeSH term(s)	Binding Sites ; Drug Discovery/methods ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Protein Interaction Domains and Motifs/drug effects ; Quantitative Structure-Activity Relationship ; Replication Protein A/antagonists & inhibitors ; Replication Protein A/chemistry ; Small Molecule Libraries
Chemical Substances	Ligands ; RPA1 protein, human ; Replication Protein A ; Small Molecule Libraries
Language	English
Publishing date	2018-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2018.10.011
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Article: Bridging the Bridging Imidazolate in the Bimetallic Center of the Cu/Zn SOD1 and ALS.

Timucin, Ahmet Can / Cinaroglu, Suleyman Selim / Sezerman, Osman Ugur / Timucin, Emel

Frontiers in chemistry

2021 Volume 9, Page(s) 716438

Abstract: Metallation status of human Cu/Zn superoxide dismutase 1 (SOD1) plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis (ALS). All of the amino acids found in the bimetallic center have been associated with ALS except for two positions. ...

Abstract	Metallation status of human Cu/Zn superoxide dismutase 1 (SOD1) plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis (ALS). All of the amino acids found in the bimetallic center have been associated with ALS except for two positions. H63 which forms the bridging imidazolate ion in the bimetallic center and K136 which is not directly involved in coordination but located in the bimetallic center were not reported to be mutated in any of the identified ALS cases. In this study, we investigated the structure and flexibility of five SOD1 variants by using classical molecular dynamics simulations. These variants include three substitutions on the non-ALS-linked positions; H63A, H63R, K136A and ALS-linked positions; G37R, H46R/H48D. We have generated four systems for each variant differing in metallation and presence of the intramolecular disulfide bond. Overall, a total of 24 different dimers including the wild-type were generated and simulated at two temperatures, 298 and 400 K. We have monitored backbone mobility, fluctuations and compactness of the dimer structures to assess whether the hypothetical mutations would behave similar to the ALS-linked variants. Results showed that particularly two mutants, H63R and K136A, drastically affected the dimer dynamics by increasing the fluctuations of the metal binding loops compared with the control mutations. Further, these variants resulted in demetallation of the dimers, highlighting probable ALS toxicity that could be elicited by the SOD1 variants of H63R and K136A. Overall, this study bridges two putative SOD1 positions in the metallic center and ALS, underlining the potential use of atomistic simulations for studying disease variants.
Language	English
Publishing date	2021-09-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711776-5
ISSN	2296-2646
ISSN	2296-2646
DOI	10.3389/fchem.2021.716438
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Article ; Online: VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization.

Gorgulla, Christoph / Çınaroğlu, Süleyman Selim / Fischer, Patrick D / Fackeldey, Konstantin / Wagner, Gerhard / Arthanari, Haribabu

International journal of molecular sciences

2021 Volume 22, Issue 11

Abstract: The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the ... ...

Abstract	The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.
MeSH term(s)	Algorithms ; Artificial Intelligence ; Computational Biology/methods ; Kelch-Like ECH-Associated Protein 1/chemistry ; Kelch-Like ECH-Associated Protein 1/metabolism ; Ligands ; Molecular Docking Simulation ; NF-E2-Related Factor 2/chemistry ; NF-E2-Related Factor 2/metabolism ; Protein Binding ; Protein Conformation ; Reproducibility of Results ; Thermodynamics
Chemical Substances	Kelch-Like ECH-Associated Protein 1 ; Ligands ; NF-E2-Related Factor 2
Language	English
Publishing date	2021-05-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22115807
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