Author: Halil Kavaklı

Our book chapter  titled “The Structure-Based Molecular-Docking Screen Against Core Clock Proteins to Identify Small Molecules to Modulate the Circadian Clock” is published  Methods in Molecular Biology.

Our book chapter  titled “Protein interaction networks of the mammalian core clock proteins” is published in Advances in Protein Chemistry and Structural Biology.

Our paper titled “Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration” is published in Functional & Integrative Genomics. This work is done with collaboration with Profs Füsun Akgül and Rıza Akgül

Our paper titled “Structure-based design and classifications of small molecules regulating the circadian rhythm period” is published in Scientific Reports. This work is done with collaboration with Prof Metin Türkay.

Our review paper is published in Current Opinion in Chemical Engineering. The review highlights recent development in drug discovery against core clock proteins.

Serefs’ preprint paper is published on BioRxiv. This paper is entitled “Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice”  and describes discovery of a molecule, M47, selectively reduces half- life of mammalian Cryptochrome 1.

M47 enhanced the effect of oxaliplatin in p53 null mouse skin fibroblast (MSF) cells.

(A) Ras pT24 transformed p53 null MEF fibroblast cells were treated with 0, 10 or 20µM oxaliplatin and incubated for 24h. Then either DMSO or M47 was added and incubated for 16h. Cells were lysed and analyzed via protein immunoblot technique. At each cases M47 increases the cleaved PARP protein level and decreases CRY1 levels. Bar graph was drawn normalizing to 10µM dosage of oxaliplatin (Data represent the mean ± SEM, n=4 **: p < 0.005, versus DMSO control by two-way ANOVA). (B) M47 in p53^−/−mice reduces age adjusted tumor incidence. Kaplan–Meier survival analysis (log-rank test) of the time of death with evidence of tumors showed significant differences between vehicle treated p53^−/− and M47 treated p53^−/− (**p<0,01)

Hande and Şeref’s collobrative paper titled “Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects” is accepted to be published in Functional & Integrative Genomics

Şeref’s paper titled “The Arg293 of Cryptochrome 1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm” is accepted to be published in Journal of Biological Chemistry.

Şeref’s paper titled “In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials” is accepted to be published in Journal of Biomolecular Structure and Dynamics.

The paper describes identification of well-tolerated and widely used drugs that have potential to be used against SARS-CoV-2

Our collaborative paper titled “Human CRY1 variants associate with attention deficit/hyperactivity disorder” where we functionally characterized CRY1-Delta6 is published in The Journal of Clinical Investigation.