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Book: Supramolecules in drug discovery and drug delivery

Mavromoustakos, Thomas / Tzakos, Andreas G. / Durdagi, Serdar

methods and protocols

(Methods in molecular biology ; 2207 ; Springer protocols)

2021

Author's details	edited by Thomas Mavromoustakos, Andreas G. Tzakos, Serdar Durdagi
Series title	Methods in molecular biology ; 2207 Springer protocols
Collection
Keywords	Biotechnology ; Pharmacology ; Materials science ; Chemistry ; Genetik, Gentechnik
Language	English
Size	xi, 344 Seiten, Illustrationen, 254 mm
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book
HBZ-ID	HT020639207
ISBN	978-1-07-160919-4 ; 9781071609200 ; 1-07-160919-X ; 1071609203
Database	Catalogue ZB MED Medicine, Health

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Article ; Online: Ab initio and comparative 3D modeling of FAM222A-encoded protein and target-driven-based virtual screening for the identification of novel therapeutics against Alzheimer's disease.

Alabdulraheem, Zeyad Tareq Jasim / Durdagi, Serdar

Journal of molecular graphics & modelling

2023 Volume 125, Page(s) 108575

Abstract: The complex nature of Alzheimer's disease (AD) makes it difficult to understand the exact molecular processes leading to neuron death. However, two molecular factors - the production of amyloid-beta plaques and tau tangles - are considered to be linked ... ...

Abstract	The complex nature of Alzheimer's disease (AD) makes it difficult to understand the exact molecular processes leading to neuron death. However, two molecular factors - the production of amyloid-beta plaques and tau tangles - are considered to be linked to AD. A genetic marker for brain atrophy, FAM222A, has been identified by the unique cross-phenotype meta-analysis of genetics imaging and the molecular features show an interaction between the protein aggregatin encoded by FAM222A and amyloid beta (Aβ)-peptide (1-42) via its N-terminal Aβ binding domain, thus increasing Aβ aggregation. Function of Aggregatin protein is unclear, and its 3D structure has not been investigated in experimental analysis, so far. Hence, in the present study, first time in literature, 3D models of FAM222A-encoded Aggregatin were systematically constructed by applying diverse homology modeling approaches and they were used as target structures at the virtual screening of FDA-approved drugs and drugs currently under research in clinical trials. Then, the identified hit molecules were chosen for further molecular dynamics (MD) simulations and post-MD analyses. Our integrated ligand-based and protein-driven-based virtual screening results show that Cefpiramide, Diniprofylline, Fostriecin, and Droperidol may target Aggregatin.
MeSH term(s)	Humans ; Alzheimer Disease/metabolism ; Amyloid beta-Peptides/chemistry ; Molecular Dynamics Simulation
Chemical Substances	Amyloid beta-Peptides
Language	English
Publishing date	2023-07-26
Publishing country	United States
Document type	Meta-Analysis ; 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.2023.108575
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Article ; Online: Developing Dynamic Structure-Based Pharmacophore and ML-Trained QSAR Models for the Discovery of Novel Resistance-Free RET Tyrosine Kinase Inhibitors.

Sayyah, Ehsan / Oktay, Lalehan / Tunç, Hüseyin / Durdagi, Serdar

ChemMedChem

2024 , Page(s) e202300644

Abstract: Activation of RET tyrosine kinase plays a critical role in the pathogenesis of various cancers, including non-small cell lung cancer, papillary thyroid cancers, multiple endocrine neoplasia type 2A and 2B (MEN2A, MEN2B), and familial medullary thyroid ... ...

Abstract	Activation of RET tyrosine kinase plays a critical role in the pathogenesis of various cancers, including non-small cell lung cancer, papillary thyroid cancers, multiple endocrine neoplasia type 2A and 2B (MEN2A, MEN2B), and familial medullary thyroid cancer. Gene fusions and point mutations in the RET proto-oncogene result in constitutive activation of RET signaling pathways. Consequently, developing effective inhibitors to target RET is of utmost importance. Small molecules have shown promise as inhibitors by binding to the kinase domain of RET and blocking its enzymatic activity. However, the emergence of resistance due to single amino acid changes poses a significant challenge. In this study, a structure-based dynamic pharmacophore-driven approach using E-pharmacophore modeling from molecular dynamics trajectories is proposed to select low energy favorable hypotheses, and ML-trained QSAR models to predict pIC50 values of compounds. For this aim, extensive small molecule libraries were screened using developed ligand-based models and potent compounds which are capable of inhibiting RET activation were proposed.
Language	English
Publishing date	2024-03-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2218496-X
ISSN	1860-7187 ; 1860-7179
ISSN (online)	1860-7187
ISSN	1860-7179
DOI	10.1002/cmdc.202300644
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Article ; Online: Covalent docking-driven virtual screening of extensive small-molecule libraries against Bruton tyrosine kinase for the identification of highly selective and potent novel therapeutic candidates.

Sambur, Ezgi / Oktay, Lalehan / Durdağı, Serdar

Journal of molecular graphics & modelling

2024 Volume 130, Page(s) 108762

Abstract: Bruton tyrosine kinases (BTKs) play critical roles in various diseases, including chronic lymphatic leukemia (CLL), Waldenström Macroglobulinemia, Marginal Zone Lymphoma, Mantle Cell Lymphoma (MCL), and Graft Versus Host diseases. BTKs are a family of ... ...

Abstract	Bruton tyrosine kinases (BTKs) play critical roles in various diseases, including chronic lymphatic leukemia (CLL), Waldenström Macroglobulinemia, Marginal Zone Lymphoma, Mantle Cell Lymphoma (MCL), and Graft Versus Host diseases. BTKs are a family of tyrosine kinases involved in B lymphocyte signal transduction, development, and maturation. Their overexpression can lead to cancer as they are essential for the activation of the B Cell Receptor (BCR) signaling pathway. Blocking the activation of BTKs presents a promising approach for treating CLL. This study was centered around the identification of small-molecule therapeutics that have an impact on human BTK. The covalently bound Ibrutinib molecule, recognized for its ability to inhibit BTK, was used as the query molecule. IUPAC text files containing molecular fragments of Ibrutinib were employed to virtually screen five different libraries comprising small-molecules, resulting in the screening of over 2.4 million synthesized compounds. Covalent docking simulations were applied to the selected small-molecules obtained through text mining from databases. Potent hit molecules capable of inhibiting BTKs through virtual screening algorithms were identified, paving the way for novel therapeutic strategies in the treatment of CLL.
Language	English
Publishing date	2024-04-04
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.2024.108762
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Article ; Online: Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interface.

Ikram, Saima / Sayyah, Ehsan / Durdagi, Serdar

Chembiochem : a European journal of chemical biology

2024 , Page(s) e202400008

Abstract: The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic ... ...

Abstract	The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic leukemia. There is considerable interest in identifying inhibitors targeting KRAS and SOS1 to explore potential therapeutic strategies for cancer treatment. In this study, advanced in silico techniques were employed to screen small molecule libraries at this interface, leading to the identification of promising lead compounds as potential SOS1 inhibitors. Comparative analysis of the average binding free energies of these predicted potent compounds with known SOS1 small molecule inhibitors revealed that the identified compounds display similar or even superior predicted binding affinities compared to the known inhibitors. These findings offer valuable insights into the potential of these compounds as candidates for further development as effective anti-cancer agents.
Language	English
Publishing date	2024-04-15
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.202400008
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Article ; Online: Virtual drug repurposing study for the CGRPR identifies pentagastrin and leuprorelin as putative candidates.

Aksoydan, Busecan / Durdagi, Serdar

Journal of molecular graphics & modelling

2022 Volume 116, Page(s) 108254

Abstract: Calcitonin gene-related peptide receptor (CGRPR) is a heterodimer consisting of CLR and RAMP1 proteins. Activation of the CGRPR with the endogenous peptide CGRP is known to play a crucial role in migraine pathophysiology. CGRP occupies two regions in the ...

Abstract	Calcitonin gene-related peptide receptor (CGRPR) is a heterodimer consisting of CLR and RAMP1 proteins. Activation of the CGRPR with the endogenous peptide CGRP is known to play a crucial role in migraine pathophysiology. CGRP occupies two regions in the CGRPR upon binding, namely ectodomain and transmembrane sites (sites 1 and 2, respectively). The disruption of the CGRPR heterodimer interface is one of the main strategies to prevent CGRPR activation and its resulting effects. So far, FDA approved monoclonal antibodies and small molecule gepant inhibitors are considered for the treatment of acute or chronic migraine symptoms. However, most of these gepants have severe side effects. Thus, in this study, a virtual drug repurposing approach is applied to CGRPR to find alternative or better molecules that would have a potential to inhibit or block the CLR - RAMP1 interface compared to known gepant molecules. A small molecule library of FDA-approved molecules was screened in these two different binding sites, further simulations were performed and analyzed. The objectives of this study are (i) to repurpose an FDA-approved drug having more potent features for CGRPR inhibition compared to gepants, and (ii) to examine whether the transmembrane binding site (site 2) accepts small molecules or small peptide analogues for binding. As a result of this extensive in silico analysis, two molecules were identified, namely pentagastrin and leuprorelin. It is shown that FDA approved compound rimegepant and the identified pentagastrin molecules form and maintain the interactions through CLR W72 and RAMP1 W74, which are the residues revealed to have an important role in CGRPR antagonism at binding site 1. At binding site 2, the interactions needed to be formed for CGRP binding are not captured by rimegepant nor leuprorelin, yet leuprorelin forms more interactions throughout the simulations, meaning that small molecules are also capable of binding to site 2. Moreover, it is found that the crucial interactions for receptor signaling and heterodimerization occurred between CLR and RAMP1 interface are disrupted more with the ligands bound to ectodomain site, rather than the transmembrane domain. These findings of pentagastrin and leuprorelin molecules are recommended to be considered in further de novo drug development and/or experimental studies related to CGRPR signaling blockade and antagonism.
MeSH term(s)	Calcitonin Gene-Related Peptide/chemistry ; Calcitonin Gene-Related Peptide/metabolism ; Calcitonin Gene-Related Peptide Receptor Antagonists ; Calcitonin Receptor-Like Protein/metabolism ; Drug Repositioning ; Leuprolide ; Pentagastrin ; Receptor Activity-Modifying Protein 1/metabolism ; Receptors, Calcitonin Gene-Related Peptide/chemistry ; Receptors, Calcitonin Gene-Related Peptide/metabolism
Chemical Substances	Calcitonin Gene-Related Peptide Receptor Antagonists ; Calcitonin Receptor-Like Protein ; Receptor Activity-Modifying Protein 1 ; Receptors, Calcitonin Gene-Related Peptide ; Pentagastrin (EF0NX91490) ; Leuprolide (EFY6W0M8TG) ; Calcitonin Gene-Related Peptide (JHB2QIZ69Z)
Language	English
Publishing date	2022-06-18
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.2022.108254
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ab Jg. 2022: Lesesaal (EG)

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Article: Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target

Durdaği, Serdar

Turk. J. Biol.

Abstract: Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here ... ...

Abstract	Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here we used a hybrid combined molecular modeling approach in virtual drug screening repurposing study to identify new compounds against this disease. One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC’s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. We used 6654 small molecules in molecular docking and top-50 docking scored compounds were initially used in short (10-ns) molecular dynamics (MD) simulations. Based on average MM/GBSA binding free energy results, long (100-ns) MD simulations were employed for the identified hits. Both binding energy results as well as crucial residues in ligand binding were also compared with a positive control TMPRSS2 inhibitor, Camostat mesylate. Based on these numerical calculations we proposed a compound (benzquercin) as strong TMPRSS2 inhibitor. If these results can be validated by in vitro and in vivo studies, benzquercin can be considered to be used as inhibitor of TMPRSS2 at the clinical studies.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #619141
Database	COVID19

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Book ; Online: Virtual Drug Repurposing Study Against SARS-CoV-2 TMPRSS2 Target

Durdagi, Serdar

2020

Abstract: ... Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, ... ...

Abstract	Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here we used a hybrid combined molecular modeling approach in virtual drug screening repurposing study to identify new compounds against this disease. One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC’s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. We used 6654 small molecules in molecular docking and top-50 docking scored compounds were initially used in short (10-ns) molecular dynamics (MD) simulations. Based on average MM/GBSA binding free energy results, long (100-ns) MD simulations were employed for the identified hits. Both binding energy results as well as crucial residues in ligand binding were also compared with a positive control TMPRSS2 inhibitor, Camostat mesylate. Based on these numerical calculations we proposed a compound (benzquercin) as strong TMPRSS2 inhibitor. If these results can be validated by in vitro and in vivo studies, benzquercin can be considered to be used as inhibitor of TMPRSS2 at the clinical studies.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12442736
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Virtual Drug Repurposing Study Against SARS-CoV-2 TMPRSS2 Target

Durdagi, Serdar

2020

Abstract	Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here we used a hybrid combined molecular modeling approach in virtual drug screening repurposing study to identify new compounds against this disease. One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC’s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. We used 6654 small molecules in molecular docking and top-50 docking scored compounds were initially used in short (10-ns) molecular dynamics (MD) simulations. Based on average MM/GBSA binding free energy results, long (100-ns) MD simulations were employed for the identified hits. Both binding energy results as well as crucial residues in ligand binding were also compared with a positive control TMPRSS2 inhibitor, Camostat mesylate. Based on these numerical calculations we proposed a compound (benzquercin) as strong TMPRSS2 inhibitor. If these results can be validated by in vitro and in vivo studies, benzquercin can be considered to be used as inhibitor of TMPRSS2 at the clinical studies.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12442736.v1
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: All-atom 500-nano seconds Molecular Dynamics Simulations of SARS-CoV-2 Spike Receptor-binding Domain bound with ACE2

Durdagi, Serdar

2020

Abstract: Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of of SARS-CoV2 Spike Protein/ACE2 complex (PDB ID: 6M0J). In order to decrease the size of the file only protein rajectories were provided. Simulation ...

Abstract	Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of of SARS-CoV2 Spike Protein/ACE2 complex (PDB ID: 6M0J). In order to decrease the size of the file only protein rajectories were provided. Simulation has been performed with Desmond. Protein was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 nano-seconds (ns) production run was performed for the simulation. for more information: durdagilab.com; serdardurdagi@gmail.com
Keywords	6M0J ; SARS-CoV2 Spike Protein/ACE2 complex ; MD Simulations ; covid19
Subject code	612
Publishing date	2020-05-12
Publishing country	eu
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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