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Article ; Online: Computational Chemistry and Molecular Modeling of Reversible MAO Inhibitors.

Yelekçi, Kemal / Erdem, Safiye Sağ

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2558, Page(s) 221–252

Abstract: Proper elucidation of drug-target interaction is one of the most significant steps at the early stages of the drug development research. Computer-aided drug design tools have substantial contribution to this stage. In this chapter, we specifically ... ...

Abstract	Proper elucidation of drug-target interaction is one of the most significant steps at the early stages of the drug development research. Computer-aided drug design tools have substantial contribution to this stage. In this chapter, we specifically concentrate on the computational methods widely used to develop reversible inhibitors for monoamine oxidase (MAO) isozymes. In this context, current computational techniques in identifying the best drug candidates showing high potency are discussed. The protocols of structure-based drug design methodologies, namely, molecular docking, in silico screening, and molecular dynamics simulations, are presented. Employing case studies of safinamide binding to MAO B, we demonstrate how to use AutoDock 4.2.6 and NAMD software packages.
MeSH term(s)	Computational Chemistry ; Isoenzymes/metabolism ; Molecular Docking Simulation ; Monoamine Oxidase/metabolism ; Monoamine Oxidase Inhibitors/chemistry ; Monoamine Oxidase Inhibitors/metabolism ; Monoamine Oxidase Inhibitors/pharmacology ; Structure-Activity Relationship
Chemical Substances	Isoenzymes ; Monoamine Oxidase Inhibitors ; Monoamine Oxidase (EC 1.4.3.4)
Language	English
Publishing date	2022-09-28
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2643-6_17
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Article ; Online: Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques.

Boumezber, Sarah / Yelekçi, Kemal

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 8, Page(s) 3607–3629

Abstract: NO, or nitric oxide, is produced by a family of enzymes called nitric oxide synthase (NOS) from L-arginine. NO regulates many physiological functions such as smooth muscle relaxation, immune defense, and memory function. The overproduction of NO by the ... ...

Abstract	NO, or nitric oxide, is produced by a family of enzymes called nitric oxide synthase (NOS) from L-arginine. NO regulates many physiological functions such as smooth muscle relaxation, immune defense, and memory function. The overproduction of NO by the neuronal isoform of nitric oxide synthase (nNOS) is implicated in neurodegeneration and neuropathic pain, making nNOS inhibition a promising therapeutic approach. Many developed nNOS inhibitors, generally L-arginine mimetics, have some issues in selectivity and bioavailability. According to earlier studies, targeting nNOS has the advantage of decreasing excess NO in the brain while avoiding the negative consequences of inhibiting the two isozymes: endothelial NOS (eNOS) and inducible NOS (iNOS). This study applied structure-based virtual screening, molecular docking, and molecular dynamics simulations to design potent and selective inhibitors against nNOS over related isoforms (eNOS and iNOS) using human X-ray crystal structures of the NOS isoforms. It was discovered that some compounds displayed a very good inhibitory potency for hnNOS and moderate selectivity for the other isozymes, eNOS and iNOS, in addition to good solubility and desirable physiochemical properties. The compounds which showed good stability and selectivity with nNOS, such as ZINC000013485422, can be interesting and informative guidance for designing more potent human nNOS inhibitors.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Nitric Oxide Synthase Type I ; Isoenzymes ; Molecular Docking Simulation ; Enzyme Inhibitors/pharmacology ; Enzyme Inhibitors/chemistry ; Nitric Oxide Synthase ; Drug Design ; Arginine
Chemical Substances	Nitric Oxide Synthase Type I (EC 1.14.13.39) ; Isoenzymes ; Enzyme Inhibitors ; Nitric Oxide Synthase (EC 1.14.13.39) ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2022-03-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2054471
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Article ; Online: Homology modeling and

Elmezayen, Ammar D / Yelekçi, Kemal

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 17, Page(s) 6396–6414

Abstract: Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting ... ...

Abstract	Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Histone Deacetylase Inhibitors/chemistry ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylases/metabolism ; Humans ; Isoenzymes ; Molecular Dynamics Simulation ; Repressor Proteins/genetics ; Reproducibility of Results
Chemical Substances	Histone Deacetylase Inhibitors ; Isoenzymes ; Repressor Proteins ; HDAC5 protein, human (EC 3.5.1.98) ; HDAC9 protein, human (EC 3.5.1.98) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2020-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1798812
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Article ; Online: Potential inhibitors of methionine aminopeptidase type II identified via structure-based pharmacophore modeling.

Albayati, Safana / Uba, Abdullahi Ibrahim / Yelekçi, Kemal

Molecular diversity

2021 Volume 26, Issue 2, Page(s) 1005–1016

Abstract: Methionine aminopeptidase (MetAP2) is a metal-containing enzyme that removes initiator methionine from the N-terminus of a newly synthesized protein. Inhibition of the enzyme is crucial in diminishing cancer growth and metastasis. Fumagillin-a natural ... ...

Abstract	Methionine aminopeptidase (MetAP2) is a metal-containing enzyme that removes initiator methionine from the N-terminus of a newly synthesized protein. Inhibition of the enzyme is crucial in diminishing cancer growth and metastasis. Fumagillin-a natural irreversible inhibitor of MetAP2-and its derivatives are used as potent MetAP2 inhibitors. However, because of their adverse effects, none of them has progressed to clinical studies. In search for potential reversible inhibitors, we built structure-based pharmacophore models using the crystal structure of MetAP2 complexed with fumagillin (PDB ID: 1BOA). The pharmacophore models were validated using Gunner-Henry scoring method. The best pharmacophore consisting of 1 H-bond donor, 1 H-bond acceptor, and 3 hydrophobic features was used to conduct pharmacophore-based virtual screening of ZINC15 database against MetAP2. The top 10 compounds with pharmacophore fit values > 3.00 were selected for further analysis. These compounds were subjected to absorption, distribution, metabolism, elimination, and toxicity (ADMET) prediction and found to have druglike properties. Furthermore, molecular docking calculations was performed on these hits using AutoDock4 to predict their binding mode and binding energy. Three diverse compounds: ZINC000014903160, ZINC000040174591, and ZINC000409110720 with respective binding energy/docking scores of - 9.22, - 9.21, and -817 kcal/mol, were submitted to 100 ns (MD) simulations using Nanoscale MD (NAMD) software. The compounds showed stable binding mode over time. Therefore, they may serve as a scaffold for further computational and experimental optimization toward the design of more potent and safer MetAP2 inhibitors.
MeSH term(s)	Aminopeptidases ; Humans ; Methionine ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Neoplasms
Chemical Substances	Methionine (AE28F7PNPL) ; Aminopeptidases (EC 3.4.11.-)
Language	English
Publishing date	2021-04-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-021-10221-7
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Zs.A 4946: Show issues

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Article ; Online: Discovery of novel isoform-selective histone deacetylases 5 and 9 inhibitors through combined ligand-based pharmacophore modeling, molecular mocking, and molecular dynamics simulations for cancer treatment.

Elmezayen, Ammar D / Al-Obaidi, Anas / Yelekçi, Kemal

Journal of molecular graphics & modelling

2021 Volume 106, Page(s) 107937

Abstract: Class IIa histone deacetylases (HDACs) 5 and 9 play crucial roles in several human disorders such as cancer, making them important targets for drug design. Continuous research is pursed to overcome the cytotoxicity side effect that comes with the ... ...

Abstract	Class IIa histone deacetylases (HDACs) 5 and 9 play crucial roles in several human disorders such as cancer, making them important targets for drug design. Continuous research is pursed to overcome the cytotoxicity side effect that comes with the currently available broad-spectrum HDACs inhibitors. Herein, common features of active HDACs inhibitors in clinical trials and use have been calculated to generate the best pharmacophore hypothesis. Guner-Henry scoring system was used to validate the generated hypotheses. Hypo1 of HDAC5 and Hypo2 of HDAC9 exhibited the most statistically significance hypotheses. Compounds with fit value of 3 and more were examined by QuickVina 2 docking tool to calculate their binding affinity toward all class IIa HDACs. A total of 6 potential selective compounds were subjected to 100 molecular dynamics (MD) simulation to examine their binding modes. The free binding energy calculations were computed according to the MM-PBSA method. Proposed selective compounds displayed good stability with their targets and thus they may offer potent leads for the designing of HDAC5 and HDAC9 isoform selective inhibitors.
MeSH term(s)	Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylases/metabolism ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Neoplasms/drug therapy ; Protein Isoforms
Chemical Substances	Histone Deacetylase Inhibitors ; Ligands ; Protein Isoforms ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2021-05-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2021.107937
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Zs.A 3491: Show issues

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Article ; Online: Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors.

Ibrahim Uba, Abdullahi / Yelekçi, Kemal

Journal of biomolecular structure & dynamics

2019 Volume 37, Issue 14, Page(s) 3627–3636

Abstract: Histone deacetylases (HDACs) are implicated in the pathology of various cancers, and their pharmacological blockade has proven to be promising in reversing the malignant phenotypes. However, lack of crystal structures of some of the human HDAC isoforms ( ... ...

Abstract	Histone deacetylases (HDACs) are implicated in the pathology of various cancers, and their pharmacological blockade has proven to be promising in reversing the malignant phenotypes. However, lack of crystal structures of some of the human HDAC isoforms (e.g., HDAC10) hinders the design of the isoform-selective inhibitor. Here, the recently solved X-ray crystal structure of
MeSH term(s)	Amino Acid Sequence ; Drug Design ; Histone Deacetylase Inhibitors/chemistry ; Histone Deacetylases/chemistry ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Reproducibility of Results ; Structural Homology, Protein
Chemical Substances	Histone Deacetylase Inhibitors ; HDAC10 protein, human (EC 3.5.1.98) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2019-01-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2018.1521747
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Article ; Online: Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10.

Uba, Abdullahi Ibrahim / Yelekçi, Kemal

Journal of biomolecular structure & dynamics

2019 Volume 38, Issue 15, Page(s) 4397–4406

Abstract: Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic ... ...

Abstract	Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of
MeSH term(s)	Animals ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylases ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Reproducibility of Results ; Zebrafish
Chemical Substances	Histone Deacetylase Inhibitors ; HDAC10 protein, human (EC 3.5.1.98) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2019-11-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2019.1691658
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Article ; Online: Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies.

Uba, Abdullahi Ibrahim / Yelekçi, Kemal

Computational biology and chemistry

2018 Volume 75, Page(s) 131–142

Abstract: Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain ... ...

Abstract	Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structure-based drug design campaign. Here, in our continuous effort to identify potentially selective HDAC6 inhibitors, structure-based virtual screening of ∼72 461 compounds was carried out using Autodock Vina. The top 100 compounds with calculated ΔG < -10 kcal/mol were manually inspected for binding mode orientation. Furthermore, the top 20 compounds with reasonable binding modes were evaluated for selectivity by further docking against HDAC6 and HDAC7 using Autodock4. Four compounds with a carboxylic fragment, displayed potential selectivity for HDAC6 over HDAC7, and were found to have good druglike and ADMET properties. Their docking complexes were then submitted to 10 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software, to examine the stability of ligand binding modes. These predicted inhibitors remained bound to HDAC6 in the presence of water and ions, and the root-mean-square deviation (RMSD), radius of gyration (Rg) and nonbond distance (protein-ligand) profiles suggested that they might be stable over time of the simulation. This study may provide scaffolds for further lead optimization towards the design of HDAC6 inhibitors with improved selectivity.
MeSH term(s)	Biocatalysis ; Carboxylic Acids/chemical synthesis ; Carboxylic Acids/chemistry ; Carboxylic Acids/pharmacology ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical ; Histone Deacetylase 6/antagonists & inhibitors ; Histone Deacetylase 6/metabolism ; Histone Deacetylase Inhibitors/chemical synthesis ; Histone Deacetylase Inhibitors/chemistry ; Histone Deacetylase Inhibitors/pharmacology ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Structure-Activity Relationship
Chemical Substances	Carboxylic Acids ; Histone Deacetylase Inhibitors ; Ligands ; HDAC6 protein, human (EC 3.5.1.98) ; Histone Deacetylase 6 (EC 3.5.1.98)
Language	English
Publishing date	2018-05-16
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2018.05.004
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Article ; Online: Pharmacophore-based virtual screening for identification of potential selective inhibitors of human histone deacetylase 6.

Uba, Abdullahi Ibrahim / Yelekçi, Kemal

Computational biology and chemistry

2018 Volume 77, Page(s) 318–330

Abstract: Histone deacetylase (HDAC) 6 plays a role in oncogenic transformation and cancer metastasis via tubulin deacetylation, making it a critical target for anticancer drug design. However, lack of selectivity shown by many of the current HDAC6 inhibitors in ... ...

Abstract	Histone deacetylase (HDAC) 6 plays a role in oncogenic transformation and cancer metastasis via tubulin deacetylation, making it a critical target for anticancer drug design. However, lack of selectivity shown by many of the current HDAC6 inhibitors in clinical use and trials prompts the continuous search for selective inhibitors. Here, 10 pharmacophore hypotheses were developed based on the 3D common features of training set of 20 HDAC inhibitors in clinical use and trials. The hypotheses were validated using a test set of another 20 HDAC inhibitors along with 400 inactive (decoys) molecules based on Güner-Henry pharmacophore scoring method. Hypothesis 1 consisting of 1 H-bond donor, 1 H-bond acceptor and 2 hydrophobic features, was used to screen "DruglikeDiverse" database using Biovia Discovery Studio 4.5. The top 10 hit compounds were selected based on the pharmacophore fit values (>3.00). Their binding affinity against HDAC6 compared to class I HDACs (1, 2, 3 & 8) and a class IIa member (HDAC7), was calculated by molecular docking using AutoDock4. The stability of binding modes of 2 potential HDAC6-selective inhibitors (ENA501965 and IBS399024) was examined by 30 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software. Both ligands showed potential stability in HDAC6 active site over time. Therefore, these may provide additional scaffolds for further optimization towards the design of safe, potent and selective HDAC6 inhibitors.
MeSH term(s)	Catalytic Domain ; Computer-Aided Design ; Drug Design ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Histone Deacetylase 6/antagonists & inhibitors ; Histone Deacetylase 6/chemistry ; Histone Deacetylase 6/metabolism ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding
Chemical Substances	Enzyme Inhibitors ; Ligands ; HDAC6 protein, human (EC 3.5.1.98) ; Histone Deacetylase 6 (EC 3.5.1.98)
Language	English
Publishing date	2018-11-02
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2018.10.016
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Article ; Online: Homology modeling of human GABA-AT and devise some novel and potent inhibitors via computer-aided drug design techniques.

Al-Obaidi, Anas / Elmezayen, Ammar D / Yelekçi, Kemal

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 11, Page(s) 4100–4110

Abstract: γ-aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which degrades γ-aminobutyric (GABA) in the brain. GABA is an important inhibitory neurotransmitter that plays important neurological roles in the brain. ... ...

Abstract	γ-aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which degrades γ-aminobutyric (GABA) in the brain. GABA is an important inhibitory neurotransmitter that plays important neurological roles in the brain. Therefore, GABA-AT is an important drug target which regulates the GABA level. Novel and potent drug development to inhibit GABA-AT is still very challenging task. In this study, we aimed to devise novel and potent inhibitors against GABA-AT using computer-aided drug design (CADD) tools. However, the human GABA-AT crystal structure is not available yet, and we built the 3D structure of human GABA-AT based on the crystal structure of pig's liver (
MeSH term(s)	Drug Design ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Transaminases ; gamma-Aminobutyric Acid
Chemical Substances	Ligands ; gamma-Aminobutyric Acid (56-12-2) ; Transaminases (EC 2.6.1.-)
Language	English
Publishing date	2020-06-08
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1774417
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