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Article ; Online: The role of machine learning method in the synthesis and biological ınvestigation of heterocyclic compounds.

Mermer, Arif

2021 Volume 26, Issue 3, Page(s) 1875–1892

Abstract: Machine learning (ML) methods have attracted increasing interest in chemistry as in all fields of science in recent years. This method is of great importance for the design of targeted bioactive compounds, especially by avoiding loss of time, money, and ... ...

Abstract	Machine learning (ML) methods have attracted increasing interest in chemistry as in all fields of science in recent years. This method is of great importance for the design of targeted bioactive compounds, especially by avoiding loss of time, money, and chemicals. There are lots of online web-based platforms such as LibSVM and OCHEM for the application of ML methods. In this paper, it has been examined the literature data on the activity predictions of heterocyclic compounds, biological activity results such as antiurease, HIV-1 Integrase, E. Coli DNA Gyrase B, and antifungal, pharmacophore-based studies, synthesis, and finding possible inhibitors using different machine learning methods.
MeSH term(s)	DNA Gyrase ; Escherichia coli ; Heterocyclic Compounds/pharmacology ; Machine Learning ; Quantitative Structure-Activity Relationship
Chemical Substances	Heterocyclic Compounds ; DNA Gyrase (EC 5.99.1.3)
Language	English
Publishing date	2021-10-20
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-021-10264-w
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Zs.A 4946: Show issues

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Article ; Online: The Importance of Rhodanine Scaffold in Medicinal Chemistry: A Comprehensive Overview.

Mermer, Arif

Mini reviews in medicinal chemistry

2020 Volume 21, Issue 6, Page(s) 738–789

Abstract: After the clinical use of epalrestat that contains a rhodanine ring, in type II diabetes mellitus and diabetic complications, rhodanin-based compounds have become an important class of heterocyclic in the field of medicinal chemistry. Various ... ...

Abstract	After the clinical use of epalrestat that contains a rhodanine ring, in type II diabetes mellitus and diabetic complications, rhodanin-based compounds have become an important class of heterocyclic in the field of medicinal chemistry. Various modifications to the rhodanine ring have led to a broad spectrum of biological activity of these compounds. Synthesis of rhodanine derivatives, depended on advenced throughput scanning hits, frequently causes potent and selective modulators of targeted enzymes or receptors, which apply their pharmacological activities through different mechanisms of action. Rhodanine-based compounds will likely stay a privileged scaffold in drug discovery because of different probability of chemical modifications of the rhodanine ring. We have, therefore reviewed their biological activities and structure activity relationship.
Language	English
Publishing date	2020-12-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2104081-3
ISSN	1875-5607 ; 1389-5575
ISSN (online)	1875-5607
ISSN	1389-5575
DOI	10.2174/1389557521666201217144954
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Zs.A 5891: Show issues

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Article ; Online: Recent advances in triazoles as tyrosinase inhibitors.

Mermer, Arif / Demirci, Serpil

European journal of medicinal chemistry

2023 Volume 259, Page(s) 115655

Abstract: The tyrosinase enzyme, which is widely found in microorganisms, animals and plants, has a significant position in melanogenesis, plays an important role in undesirable browning of fruits and vegetables, antibiotic resistance, skin pigment formation, ... ...

Abstract	The tyrosinase enzyme, which is widely found in microorganisms, animals and plants, has a significant position in melanogenesis, plays an important role in undesirable browning of fruits and vegetables, antibiotic resistance, skin pigment formation, sclerotization of cuticle, neurodegeneration, etc. Therefore, with the wide potential application fields of tyrosinase in food, agriculture, cosmetics and pharmaceutical industries, which has become the target enzyme for the development of therapeutic agents such as antibrowning, anticancer, antibacterial, skin whitening, insecticides, etc., a large number of synthetic tyrosinase inhibitors have been widely reported in recent years. The triazole ring, which has a broad spectrum of biological action, is of increasing interest in the synthesis of new tyrosinase inhibitors. In this review, tyrosinase inhibition effects, structure-activity relationships, enzyme inhibition kinetics and mechanisms of action of 1,2,3- or 1,2,4-triazole derivatives were investigated. The data gathered is anticipated to supply rational guidance and an influential strategy for the development of novel, potent and safe tyrosinase inhibitors for better practical application in the future.
MeSH term(s)	Animals ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Monophenol Monooxygenase/antagonists & inhibitors ; Plants/metabolism ; Structure-Activity Relationship ; Triazoles/chemistry ; Triazoles/pharmacology
Chemical Substances	Enzyme Inhibitors ; Monophenol Monooxygenase (EC 1.14.18.1) ; Triazoles
Language	English
Publishing date	2023-07-20
Publishing country	France
Document type	Journal Article ; Review
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2023.115655
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Zs.B 784: Show issues

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Article ; Online: Development, synthesis and validation of improved c-Myc/Max inhibitors.

Yıldırım, Sümbül / Kocabaş, Fatih / Mermer, Arif

Journal of cellular and molecular medicine

2024 Volume 28, Issue 8, Page(s) e18272

Abstract: The pathophysiological foundations of various diseases are often subject to alteration through the utilization of small compounds, rendering them invaluable tools for the exploration and advancement of novel therapeutic strategies. Within the scope of ... ...

Abstract	The pathophysiological foundations of various diseases are often subject to alteration through the utilization of small compounds, rendering them invaluable tools for the exploration and advancement of novel therapeutic strategies. Within the scope of this study, we meticulously curated a diverse library of novel small compounds meticulously designed to specifically target the c-Myc/Max complex. We conducted in vitro examinations of novel c-Myc inhibitors across a spectrum of cancer cell lines, including PANC1 (pancreatic adenocarcinoma), MCF7 (breast carcinoma), DU-145 (prostate carcinoma), and A549 (lung cancer). The initial analysis involved a 25 μM dose, which enabled the identification of potent anticancer compounds effective against a variety of tumour types. We identified c-Myc inhibitors with remarkable potency, featuring IC50 values as low as 1.6 μM and up to 40 times more effective than the reference molecule in diminishing cancer cell viability. Notably, c-Myc-i7 exhibited exceptional selectivity, displaying 37-fold and 59-fold preference for targeting prostate and breast cancers, respectively, over healthy cells. Additionally, we constructed drug-likeness models. This study underscores the potential for in vitro investigations of various tumour types using novel c-Myc inhibitors to yield ground-breaking and efficacious anticancer compounds.
MeSH term(s)	Male ; Humans ; Adenocarcinoma ; Pancreatic Neoplasms ; Cell Line ; Cell Nucleus ; Cell Survival
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2074559-X
ISSN	1582-4934 ; 1582-4934 ; 1582-1838
ISSN (online)	1582-4934
ISSN	1582-4934 ; 1582-1838
DOI	10.1111/jcmm.18272
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Zs.A 5752: Show issues

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Article ; Online: Development of novel 1,2,4-triazole containing compounds with anticancer and potent anti-CB1 activity.

Yıldırım, Sümbül / Ayvaz, Aslıhan / Mermer, Arif / Kocabaş, Fatih

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 8, Page(s) 3862–3873

Abstract: There is still an unmet need for novel and improved anti-cancer compounds. Nitrogen atoms have heterocyclic ring moieties, which have been shown to have powerful anticancer properties in both natural and synthetic derivatives. Due to their dipole ... ...

Abstract	There is still an unmet need for novel and improved anti-cancer compounds. Nitrogen atoms have heterocyclic ring moieties, which have been shown to have powerful anticancer properties in both natural and synthetic derivatives. Due to their dipole character, hydrogen bonding capacity, rigidity and solubility, 1,2,4-triazoles are particularly effective pharmacophores, interacting with biological receptors with high affinity. Thus, novel 1,2,4-triazole-containing molecular derivatives were synthesized using green chemistry methods, microwave irradiation and ultrasonication, and these methods' operational simplicity and maximum greener synthetic efficiency with green chemistry metrics calculations will be attractive for academic and industrial research and tested against three distinct human cancer cell lines including PANC1 (pancreatic cancer), DU145 (prostate cancer), MCF7 (breast cancer) and one fibroblast cell line (HDF). Here, we showed that compounds
MeSH term(s)	Humans ; Triazoles/chemistry ; Triazoles/pharmacology ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/chemistry ; Cell Line, Tumor ; Molecular Docking Simulation ; Structure-Activity Relationship ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Molecular Dynamics Simulation ; Molecular Structure
Chemical Substances	Triazoles ; Antineoplastic Agents ; 1,2,4-triazole (288-88-0)
Language	English
Publishing date	2023-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2239909
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Zs.A 2093: Show issues

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Article ; Online: Synthesis, characterization, DFT calculation, antioxidant activity, ADMET and molecular docking of thiosemicarbazide derivatives and their Cu (II) complexes.

Mermer, Arif / Alyar, Saliha

Chemico-biological interactions

2021 Volume 351, Page(s) 109742

Abstract: In this work, new thiosemicarbazides (ECA-1, ECA-2) and their Cu (II) complexes (ECA-1-Cu, ECA-2-Cu) were synthesized and their structures were characterized ... ...

Abstract	In this work, new thiosemicarbazides (ECA-1, ECA-2) and their Cu (II) complexes (ECA-1-Cu, ECA-2-Cu) were synthesized and their structures were characterized by
MeSH term(s)	Antioxidants/chemical synthesis ; Antioxidants/chemistry ; Antioxidants/metabolism ; Antioxidants/pharmacokinetics ; Coordination Complexes/chemical synthesis ; Coordination Complexes/chemistry ; Coordination Complexes/metabolism ; Coordination Complexes/pharmacokinetics ; Copper/chemistry ; Density Functional Theory ; Humans ; Ligands ; Models, Chemical ; Molecular Docking Simulation ; Peroxiredoxins/metabolism ; Protein Binding ; Semicarbazides/chemical synthesis ; Semicarbazides/chemistry ; Semicarbazides/metabolism ; Semicarbazides/pharmacokinetics
Chemical Substances	Antioxidants ; Coordination Complexes ; Ligands ; Semicarbazides ; Copper (789U1901C5) ; PRDX2 protein, human (EC 1.11.1.15) ; Peroxiredoxins (EC 1.11.1.15)
Language	English
Publishing date	2021-11-11
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	218799-1
ISSN	1872-7786 ; 0009-2797
ISSN (online)	1872-7786
ISSN	0009-2797
DOI	10.1016/j.cbi.2021.109742
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Zs.A 686: Show issues

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Article ; Online: Exploring the Anti-Cancer Potential of Hispidin: A Comprehensive in Silico and in Vitro Study on Human Osteosarcoma Saos2 Cells.

Benarous, Khedidja / Serseg, Talia / Mermer, Arif / Tahmasebifar, Aydin / Boulebd, Houssem / Linani, Abderahmane

Chemistry & biodiversity

2024 , Page(s) e202301833

Abstract: Hispidin was initially discovered in basidiomycete Inonotus hispidus (Bull.) P. Karst and this extraordinary compound possesses immense potency and can be extracted from the wild mushroom through specialized bioreactor cultivation techniques. In our ... ...

Abstract	Hispidin was initially discovered in basidiomycete Inonotus hispidus (Bull.) P. Karst and this extraordinary compound possesses immense potency and can be extracted from the wild mushroom through specialized bioreactor cultivation techniques. In our study, we isolated it from Inonotus hispidus (Bull.) P. Karst., with a yield of 3.6 %. We identified and characterized hispidin through the implementation of spectroscopic techniques such as FTIR, NMR, and MS. Additionally, we utilized Thermogravimetric Analysis for thermal characterization of the compound. Computational studies based on DFT were performed to investigate the molecular structure, electronic properties, and chemical reactivity of hispidin. PASS analysis for hispidin demonstrated that 19 of them are anti-neoplastic activities. The Pharmacology prediction of hispidin confirm that it is not toxic, non-carcinogenesis with a good human intestinal absorption. The effect of hispidin on the viability of bone cancer cells was evaluated by MTT assay. The results showed that hispidin significantly reduced SaoS2 cell viability in a dose-dependent manner. Molecular docking was carried out using five targets related to bone cancer to determine the interactions between hispidin and the studied proteins. The results demonstrate that hispidin is a good inhibitor for the five targets. Dynamic simulation shows a good stability of the complex hispidin-protein.
Language	English
Publishing date	2024-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2139001-0
ISSN	1612-1880 ; 1612-1872
ISSN (online)	1612-1880
ISSN	1612-1872
DOI	10.1002/cbdv.202301833
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Article ; Online: Synthesis and evaluation of the antioxidant and anti-tyrosinase activities of thiazolyl hydrazone derivatives and their application in the anti-browning of fresh-cut potato

Djafarou, Selsabil / Mermer, Arif / Barut, Burak / Yılmaz, Gizem Tatar / Amine khodja, Imene / Boulebd, Houssem

Food Chemistry. 2023 July, v. 414 p.135745-

2023

Abstract: Tyrosinase is a key enzyme in the biosynthesis of melanin, which is responsible for the browning of foods as well as many skin disorders. In order to develop new anti-browning agents with dual antioxidant and anti-tyrosinase capacities, a series of 30 ... ...

Abstract	Tyrosinase is a key enzyme in the biosynthesis of melanin, which is responsible for the browning of foods as well as many skin disorders. In order to develop new anti-browning agents with dual antioxidant and anti-tyrosinase capacities, a series of 30 thiazolyl hydrazone derivatives were synthesized. Among the molecules prepared, 6 and 30 were found to be the most potent tyrosinase inhibitors with IC₅₀ values comparable to that of kojic acid. Interestingly, 6 also has the highest radical scavenging activity among the prepared molecules. The inhibition kinetics study indicated that 6 is a non-competitive inhibitor while 30 inhibits tyrosinase competitively. The anti-browning assay of fresh-cut potato slices revealed that 6 and 30 are potent anti-browning agents with a capacity as high as kojic acid. The mechanisms of free radical scavenging and tyrosinase inhibition have been fully investigated in silico using computational kinetics, molecular docking, and molecular dynamics simulations.
Keywords	antioxidants ; biosynthesis ; computer simulation ; enzymes ; food chemistry ; free radicals ; hydrazones ; kojic acid ; melanin ; molecular dynamics ; potatoes ; Thiazolyl hydrazine ; Anti-tyrosinase ; Anti-browning ; DFT calculations ; Molecular modeling
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2023.135745
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Article ; Online: Recent studies of nitrogen containing heterocyclic compounds as novel antiviral agents: A review.

Mermer, Arif / Keles, Turgut / Sirin, Yakup

Bioorganic chemistry

2021 Volume 114, Page(s) 105076

Abstract: N-heterocycles are important, not only because of their abundance, but above all because of their chemical, biological and technical significance. They play an important role in biological investigation such as anticancer, antiinflammatory, antibacterial, ...

Abstract	N-heterocycles are important, not only because of their abundance, but above all because of their chemical, biological and technical significance. They play an important role in biological investigation such as anticancer, antiinflammatory, antibacterial, antiviral, anti-tumor, antidiabetic, etc. In this study, we focused on examining synthesized some 5- or 6-ring N-heterocyclic compounds that showed the antiviral activity in last 5 years, and investigation of these compounds structure-activity relationship studies. This review will be useful to scientists in research fields of organic synthesis, medicinal chemistry, and pharmacology.
MeSH term(s)	Antiviral Agents/chemical synthesis ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Heterocyclic Compounds/chemical synthesis ; Heterocyclic Compounds/chemistry ; Heterocyclic Compounds/pharmacology ; Humans ; Microbial Sensitivity Tests ; Nitrogen/chemistry ; Nitrogen/pharmacology ; Viruses/drug effects
Chemical Substances	Antiviral Agents ; Heterocyclic Compounds ; Nitrogen (N762921K75)
Language	English
Publishing date	2021-06-10
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2021.105076
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Zs.A 4207: Show issues

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Article ; Online: Synthesis of novel pancreatic lipase inhibitors: Biological investigation and

Mermer, Arif / Demirci, Serpil / Tatar, Gizem

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 2, Page(s) 931–940

Abstract: The targeted compounds which are Schiff base derivatives were prepared by reaction of 6-(4-phenyl-piperazin-1-yl)pyridine-3-ylamine with 2-hydroxy and 2,6-dichloro benzaldehyde. These compounds were isolated, purified and then spectrally characterized ... ...

Abstract	The targeted compounds which are Schiff base derivatives were prepared by reaction of 6-(4-phenyl-piperazin-1-yl)pyridine-3-ylamine with 2-hydroxy and 2,6-dichloro benzaldehyde. These compounds were isolated, purified and then spectrally characterized via FT-IR,
MeSH term(s)	Animals ; Enzyme Inhibitors/chemistry ; Lipase/chemistry ; Molecular Docking Simulation ; Pancreas ; Spectroscopy, Fourier Transform Infrared ; Swine
Chemical Substances	Enzyme Inhibitors ; Lipase (EC 3.1.1.3)
Language	English
Publishing date	2021-07-11
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1950573
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