The influence of glycerol on the binding of methotrexate toMycobacterium tuberculosisdihydrofolate reductase: a molecular modelling study

Abstract

2015): The influence of glycerol on the binding of methotrexate to Mycobacterium tuberculosis dihydrofolate reductase: a molecular modelling study, Molecular Simulation, The enzyme, dihydrofolate reductase (DHFR), from Mycobacterium tuberculosis (mt-DHFR) is believed to be a potential drug target for the treatment of tuberculosis. The co-crystal structure of mt-DHFR bound with glycerol (GOL), NAPDH and methotrexate (MTX) reveals a GOL binding site on the enzyme. This GOL binding site could be very important for the design of novel, selective mt-DHFR inhibitors, because this binding site is absent on human DHFR (h-DHFR). We have performed molecular dynamic simulations and free energy calculations to evaluate the binding affinity of GOL and its free energy contribution to the binding of MTX to mt-DHFR. The results showed that GOL does not bind tightly to mt-DHFR. Although GOL itself contributed free energy on MTX binding to mt-DHFR, GOL also increased the flexibilities of MTX, so that MTX cannot maintain strong electronic interactions with ARG32 and ARG60, which caused the total binding free energy to decrease. These data suggest that GOL binding is weak and it could be expelled from the binding site, to allow inhibitors containing appropriate side chains to bind. This observation can be used to inform future drug design studies, especially those aimed at improving drug selectivity against h-DHFR.

Selective Non-toxics Inhibitors Targeting DHFR for Tuberculosis and Cancer Therapy: Pharmacophore Generation and Molecular Dynamics Simulation

“…As a positive control, five known and Food and Drug Administration (FDA)-approved inhibitors that have inhibitory activity against the target protein and the natural substrate (dihydrofolate) were selected, all five inhibitors of reference have shown a good affinity toward the enzyme, the most potent one is MTX that showed the lowest value of affinity energy (–8.9 kcal/mol), this molecule is used usually as an anticancer drug, 7 based on the aforementioned information, MTX was taken as the inhibitor of reference in terms of energy score to compare its activity and potency with the 11 selected molecules.…”

“…The inhibition of DHFR is the basis for the use of MTX as a cancer chemotherapy drug. 7 In our study, we approved the toxic profile of this drug using in silico approach, MTX was found to be in class 1 in toxicity level with an LD50 of 3 mg/ kg, which was approved by another study; a meta-analysis reported across Asian, Caucasian, pediatric, and adult patients that treats three systematic reviews on MTX-induced toxicity, 33 another research on MTX doses described that MTX is administered at doses ranged from 12 mg intrathecally and 20 mg/m 2 orally, or intravenously as weekly maintenance chemotherapy for all to doses as high as 33 000 mg/m 2 , higher given intravenously are defined as high-dose MTX (HDMTX) therapy that can cause significant toxicity, which not only leads to morbidity and occasional mortality but may also interrupt cancer treatment. 34 Searching for a non-toxic alternative drug that has a better affinity than MTX for h-DHFR was the second part of this study.…”

“…This inhibition is the basis for the use of MTX in cancer chemotherapy and it has been widely used in the past for the treatment of a variety of malignancies, including breast, head and neck, leukemia, lymphoma, lung, osteosarcoma, bladder, and trophoblastic neoplasms. 7,8 Nevertheless, MTX is not selective for mt-DHFR 9. Trimethoprim (TMP) and pyrimethamine (PYR) are selective and powerful inhibitors of protozoan DHFR, 9,10 but they have a low affinity for mt-DHFR.…”