Molecular Dynamics Simulation Reveal the Mechanism of Resistance of Mutant Actins to Latrunculin A - Insight into Specific Modifications to Design Novel Drugs to Overcome Resistance.

BACKGROUND: Mutant actins D157E and R183A-D184A are reported to resist the anticancer drug Latrunculin A (LAT); though identified, the mechanism of resistance is not clearly understood. OBJECTIVE: To design better molecules that can overcome the resistance caused by mutations it is important to define precise pharmacophoric regions in LAT based on the mechanism of resistance on the mutant actin -LAT interactions. METHODS: To address this we have conducted 20 nano seconds (ns) simulation of mutant actins - LAT complex and compared it with the 20ns simulation of wild actin - LAT complex. Functions as the binding free energy, distance between LAT and binding site residues, LAT and actin domains, dihedral angle analysis, motional correlation were studied of these simulations. RESULTS: Grounded on these studies, four sites in LAT are identified to be crucial for modification. Bulkier ring moieties containing nitrogen in place of the double bonded oxygen in the macrocyclic lactone ring may be considered to establish interactions with Glu214. The nitrogen in 2-thiazolidinone moiety can be substituted with a hydrophobic ring to stabilise the interaction with the Asp157Glu and the oxygen in the cyclohexane of LAT with hydrophilic groups to strengthen their interaction with Tyr69. The nitrogen of the 2-thiazolidinone moiety can be replaced with nitrogen containing rings to improve inhibition of the actin polymerisation. Apart from this chemical groups on the sulphur of 2-thiazolidinone moiety to improve the hydrophobic interaction with actin is also identified for modification. CONCLUSION: Based on this a combinatorial library of 46 LAT analogs was generated and docked with the wild and mutant actins to identify potent leads to become anti-actin anticancer drugs.

Molecular dynamics and high throughput binding free energy calculation of anti-actin anticancer drugs-New insights for better design.

Actin cytoskeleton plays an important role in cancerous cell progression. Till date many anticancer toxins are discovered that binds to different sites of actin. Mechanism of action of these toxins varies with respect to the site where they bind to actin. Latrunculin A (LAT) binds closely to nucleotide binding site and Reidispongiolide binds to the barbed end of actin. LAT is reported to reduce the displacement of domain 2 with respect to domain 1 and allosterically modulate nucleotide exchange. On the other hand Reidispongiolide binds with the higher affinity to actin and competes with the DNaseI binding loop once the inter-monomer interaction has been formed. Evolving better actin binders being the aim of this study we conducted a comparative molecular dynamics of these two actin-drug complexes and actin complexed with ATP alone, 50ns each. High throughput binding free energy calculations in conjugation with the high-throughput MD simulations was used to predict modifications in these two renowned anti-actin anticancer drugs for better design. Per residue energy profiling that contribute to free energy of binding shows that there is an unfavourable energy at the site where Asp157 interacts with 2-thiazolidinone moiety of LAT. Similarly, unfavourable energies are reported near macrocyclic region of Reidispongiolide specifically near carbons 7, 11 & 25 and tail region carbons 27 & 30. These predicted sites can be used for modifications and few of these are discussed in this work based on the interactions with the binding site residues. The study reveals specific interactions that are involved in the allosteric modulation of ATP by these two compounds. Glu207 closely interacting with LAT A initiates the allosteric effect on ATP binding site specifically affecting residues Asp184, Lys215 and Lys336. RGA bound actin shows high anti-correlated motions between sub domain 3 and 4. Unlike LAT A, Reidispongiolide induces a flat structure of actin which definitely should affect actin polymerisation and lead to disassembly of actin filaments.