Seyit Kale

Dr. Seyit Kale

orcid

Research Focus & Metrics

Academic Career Length

15Years (2012-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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16 August 2023 in Trends in Biochemical Sciences
Verified
Journal Article
Closed access
SKSeyit Kale
Seyit Kale
RBRamachandran Boopathi
Ramachandran Boopathi
EBEdwige Belotti
Edwige Belotti
ILImtiaz Nisar Lone
Imtiaz Nisar Lone
MGMohamed Graies
Mohamed Graies
SDStefan Dimitrov
Stefan Dimitrov

19 April 2017 in Chemical Science
Verified
Journal Article
Open access
PDF file
CBChen Bai
Chen Bai
SKSeyit Kale
Seyit Kale
JHJudith Herzfeld
Judith Herzfeld
For a century now, “Lewis dots” have been a mainstay of chemical thinking, teaching and communication. However, chemists have assumed that this semi-classical picture of electrons needs to be abandoned for quantitative work, and the recourse in computational simulations has been to the extremes of first principles treatments of electrons on the one hand and force fields that avoid explicit electrons on the other hand. Given both the successes and limitations of these highly divergent approaches, it seems worth considering whether the Lewis dot picture might be made quantitative after all. Here we review progress to that end, including variations that have been implemented and examples of applications, specifically the acid–base behavior of water, several organic reactions, and electron dynamics in silicon fracture. In each case, the semi-classical approach is highly efficient and generates reasonable and readily interpreted reaction trajectories in turnkey fashion (i.e., without any input about products). Avenues for further progress are also discussed.

1 March 2021 in Journal of Molecular Biology
Verified
Journal Article
Closed access
DDDeniz Doğan
Deniz Doğan
MAMerve Arslan
Merve Arslan
TUTuğçe Uluçay
Tuğçe Uluçay
SKSibel Kalyoncu
Sibel Kalyoncu
SDStefan Dimitrov
Stefan Dimitrov
SKSeyit Kale
Seyit Kale

6 January 2023 in Structure
Verified
Journal Article
Closed access
JLJaime Alegrio Louro
Jaime Alegrio Louro
RBRamachandran Boopathi
Ramachandran Boopathi
BBBrice Beinsteiner
Brice Beinsteiner
APAbdul Kareem Mohideen Patel
Abdul Kareem Mohideen Patel
TCTat Cheung Cheng
Tat Cheung Cheng
SDStefan Dimitrov
Stefan Dimitrov

25 October 2024 in Cancers
Verified
Journal Article
Open access
PDF file
SASadaf Asfa
Sadaf Asfa
RBReza Arshinchi Bonab
Reza Arshinchi Bonab
OÖOnur ÖNDER
Onur ÖNDER
MAMerve Uça Apaydin
Merve Uça Apaydin
HDHatice Döşeme
Hatice Döşeme
APAthanasia Pavlopoulou
Athanasia Pavlopoulou
Background/Objectives: Acute myeloid leukemia (AML) is characterized by therapeutic failure and long-term risk for disease relapses. As several therapeutic targets participate in networks, they can rewire to eventually evade single-target drugs. Hence, multi-targeting approaches are considered on the expectation that interference with many different components could synergistically hinder activation of alternative pathways and demolish the network one-off, leading to complete disease remission. Methods: Herein, we established a network-based, computer-aided approach for the rational design of drug combinations and de novo agents that interact with many AML network components simultaneously. Results: A reconstructed AML network guided the selection of suitable protein hubs and corresponding multi-targeting strategies. For proteins responsive to existing drugs, a greedy algorithm identified the minimum amount of compounds targeting the maximum number of hubs. We predicted permissible combinations of amiodarone, artenimol, fostamatinib, ponatinib, procaine, and vismodegib that interfere with 3–8 hubs, and we elucidated the pharmacological mode of action of procaine on DNMT3A. For proteins that do not respond to any approved drugs, namely cyclins A1, D2, and E1, we used structure-based de novo drug design to generate a novel triple-targeting compound of the chemical formula C15H15NO5, with favorable pharmacological and drug-like properties. Conclusions: Overall, by integrating network and structural pharmacology with molecular modeling, we determined two complementary strategies with the potential to annihilate the AML network, one in the form of repurposable drug combinations and the other as a de novo synthesized triple-targeting agent. These target–drug interactions could be prioritized for preclinical and clinical testing toward precision medicine for AML.

4 October 2012 in Angewandte Chemie
Verified
Journal Article
Closed access
PDF file
SKSeyit Kale
Seyit Kale
DHDr. Judith Herzfeld
Dr. Judith Herzfeld