The computational study on the elucidation of the binding interactions and mechanism of anti-neoplastic purine derivative drugs with DNA: Molecular docking and md simulation studies

Abstract

This Ph.D. thesis has begun to discover how to defeat cancer by causing apoptosis via studying the DNA binding mechanism of anticancer (antineoplastic) drugs. To do that, mechanisms should have been revealed regarding the silencing of specific nucleotides within the genes and/or breaking the double helix of cancerous cell DNA via performing molecular docking and molecular dynamics simulations to understand how chemical interactions and functional groups play roles in the binding of anticancer drugs to DNA. Fludarabine, Pemetrexed, Cladribine, Clofarabine, and Azacitidine, are very well-known marketed, significant anticancer medicinal drugs falling under the antimetabolite Purine analog drug class. Although these drugs were used in the past with FDA approval for treating various cancer types, their main indications for DNA binding, nucleotide regioselectivity, and mode of binding on DNA have not been discovered in detail yet in the scientific literature. Therefore, how they can be further developed from the perspective of altering the functional groups according to the laws and tools of pharmaceutical chemistry, organic chemistry, analytical chemistry, and computational in-silico drug design were deciphered with this Ph.D. thesis and supported with the research articles published along with it. The above-mentioned Purine analog drugs are generally considered to be a group of agents with similar structures, possessing slightly different mechanisms of action, indications, and side effects. These agents are nucleoside analogs and are considered antimetabolites that interfere with or compete with nucleoside triphosphates in the synthesis of DNA or RNA or both. The substances are analogs of adenine or guanine and generally have excellent activity against chronic lymphocytic leukemia, acute lymphoblastic leukemia, acute myeloid-lymphoma leukemias, and small lymphocytic leukemia due to their preferential uptake, activation, and action in lymphoid tissue. These drugs act by interacting with the cancerous cell DNA by turning off its function and protein expression. Hence, the binding interactions of these drugs with DNA in the chemical and pharmaceutical industry are significant topics for pharmaceutical, medical, bio/genetic engineering, and biochemical studies aimed at designing better DNA binding drugs. The discovery of how these drugs dock onto which region and nucleotide of DNA and the mechanism by which drugs bind to DNA are essential in discovering how to synthesize new drugs and learn how to make their indications perfect. A systematic general scheme and model of how drugs bind to DNA and which functional groups in drugs bind to which DNA nucleotide with which affinities were formed with this thesis, thus the contribution to the pathways of new drug design discovery and drug use methodology was made. Before the drugs go into production, it will now be possible to know how the chemical structures of other drugs and new pharmaceutical drugs on the market should be in terms of studied functional groups, and what the DNA binding mechanism of the designed drugs might be, thanks to this schematic inferred information. All over the world, the pharmaceutical industry spends hundreds of billions of dollars on new research settings that can synthesize efficiently, high-yield, non-toxic drugs possessing correct indications. Each antineoplastic drug requires an average of two to three billion dollars in research and development costs and at least 10 to 15 years for its indication to be approved by the FDA. Synthesizing specific antineoplastic drugs for the receptor target plays a crucial role in terms of saving time and money. Studying human DNA and antineoplastic drugs targeting it, which is the most significant of these receptors, is a very essential research topic on a global scale. Thanks to this Ph.D. thesis and the published research articles produced from the subject of the thesis, a methodological system that can determine the indication mechanism, nucleotide regioselectivity, and binding type before synthesizing the drug had been created, thus as all the scientists aim in the future, a contribution may be made with this study on revoking the animal and human drug trial phases and can reduce the time loss that causes billions of dollars and immeasurable years spent in the research of antineoplastic drugs. Finding such a way to predict the mechanisms of these drugs, using various computational and simulation techniques, would greatly contribute to the national and world drug economy and scientific knowledge library. Since this is a very comprehensive theoretical study also involving the comparison of experimental results, it is believed that it will pioneer and shed light on future studies in this area. The DNA interactions of the aforementioned 5 important cancer drugs have not been investigated in detail yet in the scientific literature. Therefore, this Ph.D. thesis study focuses on the binding properties of drugs with molecular dynamics (MD) simulations as well as molecular docking studies. Therefore, it was determined which region of the drug attacks which nucleotide of the cancer cell DNA and destroys the cancer cell DNA. The unique value of this Ph.D. thesis was the discovery of the ability and capacity of the cancer drugs we studied to break down cancerous cell DNA by interacting directly with it. How this happens and what the actual mechanisms are for each drug have been examined in detail with both theoretical and experimental results in order to reveal them. The mechanisms of action of DNA fragmentation of such 5 important drugs in the pharmaceutical and chemistry world were not known in such detail, and in addition, it was not known which part of the DNA of the groups in the chemical structures of these drugs and how they interact. With the aid of such research, how these drugs can be developed further for more efficiency and how cancer cell DNA can be destroyed with more selectivity with the aid of studied functional groups have been now revealed through my work. It will be possible to accurately predict the DNA binding pattern, indication, activity, stability, and degree of DNA denaturation of any drug produced or to be produced in the future, just by checking its chemical structure. The main objective of this thesis was to research which drug matches which binding pattern and therefore to determine the DNA binding affinity and efficiency of the drugs of interest. This knowledge, computed theoretically and compared with the results of multispectroscopic experimental studies, has revealed the capabilities of hitherto unknown mechanisms of antineoplastic drugs. To achieve such a goal, the effectiveness of interactions appears to depend on various factors, including the affinity of the drug's external groups to DNA, and the topology of the binding. The mechanisms of these interactions are basically divided into four groups. The first is gene silencing by direct covalent binding of the drug to the backbone and nucleotides of the DNA, the second is gene silencing by non-covalent chemical interactions, and the third is the intercalation mechanism in which the drug gets stuck between the base pairs of the DNA and breaks down the DNA like a zipper, and the fourth is the groove binding mechanism to silence the DNA gene expression via minor and/or major groove binding that can shut down DNA completely. By simulating and computing the theoretical stability and binding energies of such drugs docked onto DNA, there made be a comparison with multispectroscopic experimental findings to ensure the binding mode and efficacy. Finding out which drug has which mode of binding reveals the effectiveness of systematical silencing/cleavage (by intercalation or groove binding) of the DNA in the cancer cell. By doing so, it can be predicted that an antineoplastic drug can attack which part of the DNA in the cancerous cell and lead the cancerous cell to apoptosis, even by theoretically drawing its chemical structure at the design stage. It is found with this Ph.D. thesis that Fludarabine suppresses the DNA via major groove binding, while Pemetrexed, Cladribine, and Clofarabine do it by minor groove binding whereas Azacitidine is an intercalator agent and unzips the helical structure of DNA completely. It is drawn from the pharmaceutical chemistry analysis of such massive data that when a Fluorine replacement takes place in the Purine ring of the aforementioned drugs, adenylation type of nucleotide-binding occurs whereas when Carboxylation, Methylation, and Hydroxylation take place in the Purine ring, poly-adenylation occurs. When a Chlorine replacement takes place in the Ribose ring, Guanidinylation ends and Adenylation occurs. Also, Chlorine replacement in the Ribose ring causes the mode of binding alteration from minor to major groove.