Relative residence time estimation of small allosteric modulators. (Presentación oral)

BARRERA GUISASOLA, EXEQUIEL E.; BUSTOS DIEGO M.

Congreso; XI Argentine Congress of Bioinformatics and Computational Biology.; 2021

Background:Computationalmethods are vastly used in the search of drug candidates both inacademia and the pharmacological industry. One of the principalcriterium to select small compounds is by estimating their bindingaffinity to target macromolecules of interest. Common practicebinding affinity calculations can be classified in a broad spectra ofaccuracy and computational costs. Starting from molecular docking, tomore detailed molecular dynamics derived techniques such as MM/GBSAor Umbrella Sampling, up to the most accurate myriad of hybridquantum QM/MM methods. A recent alternative to these thermodynamicsapproaches proposes changing the focus towards kinetic properties,searching specifically for compounds with longer residence times,that highly correlate with their efficacy and selectivity. In thiswork, we employed the tau Random Accelerated Molecular Dynamics(τRAMD). Briefly, this technique applies random forces over thecenter of mass of the ligand, accelerating its egress process.Averaged residence times of multiple simulated replicas highlycorrelate with experimental data. Our main goal is to evaluate thepredictive behavior of the technique on different small compoundsthat could allosterically modulate 14-3-3, a protein that interactswith phosphorylated proteins regulating multiple cellular processeslike apoptosis and cell differentiation, just to name a few of them.Results:Weperformed atomistic MD simulations of the εparalog of 14-3-3 in its apo-form and with norharmane bound to itsallosteric site. Norharmane is an unsubstituted β-carbolineand we selected it as our lead compound. In the presence of theligand, 14-3-3 remained locked in a closed state, different from theapo system which fluctuated between opened and closed states. Thedescribed behavior was quantified by performing a solvent accessiblesurface area analysis of the amphipathic groove, that corresponds tothe region where phosphorylated partners bind. For the relativeresidence time (τ) calculations we first evaluate forces ofdifferent magnitudes. Starting with 14 kcal.mol-1.Å-1, that resultedin extremely short τ. This could be explained by the shallow shapeof the binding pocket. Forces of 2.4 kcal.mol-1.Å-1 were the moreappropriate for our system, resulting in τ = 0.58 ±0.2 ns.A set of substituted β-carbolineswere later docked into the allosteric site and their relativeresidence times were measured with τRAMD. Seeking selectivity, weemployed the same set of compounds to study on a different paralog,14-3-3 γ.Conclusions:Weobserved how norharmane can allosterically regulate theconformational behavior of 14-3-3, locking its amphipathic grooveinto a closed state. The τRAMD technique was fine-tuned for ourspecific system and substituted β-carbolinespresenting the highest residence times for each paralog have beenchosen to be examined in further experimental studies.p { margin-bottom: 0.1in; direction: ltr; color: #000000; line-height: 115%; text-align: left; orphans: 2; widows: 2 }p.western { font-family: "Liberation Serif", serif; font-size: 12pt; so-language: en-US }p.cjk { font-family: "Noto Sans CJK SC"; font-size: 12pt; so-language: zh-CN }p.ctl { font-family: "Lohit Devanagari"; font-size: 12pt; so-language: hi-IN }