Computational study of the activity, dynamics, energetics and conformations of insulin analogues using molecular dynamics simulations: Application to hyperinsulinemia and the critical residue B26

Abstract

Due to the increasing prevalence of diabetes, finding therapeutic analogues for insulin has become an urgent issue. While many experimental studies have been performed towards this end, they have limited scope to examine all aspects of the effect of a mutation. Computational studies can help to overcome these limitations, however, relatively few studies that focus on insulin analogues have been performed to date. Here, we present a comprehensive computational study of insulin analogues—three mutant insulins that have been identified with hyperinsulinemia and three mutations on the critical B26 residue that exhibit similar binding affinity to the insulin receptor—using molecular dynamics simulations with the aim of predicting how mutations of insulin affect its activity, dynamics, energetics and conformations. The time evolution of the conformers is studied in long simulations. The probability density function and potential of mean force calculations are performed on each insulin analogue to unravel the effect of mutations on the dynamics and energetics of insulin activation. Our conformational study can decrypt the key features and molecular mechanisms that are responsible for an enhanced or reduced activity of an insulin analogue. We find two key results: 1) hyperinsulinemia may be due to the drastically reduced activity (and binding affinity) of the mutant insulins. 2) Y26BS and Y26BE are promising therapeutic candidates for insulin as they are more active than WT-insulin. The analysis in this work can be readily applied to any set of mutations on insulin to guide development of more effective therapeutic analogues.

Progress in Simulation Studies of Insulin Structure and Function

“…Specifically, the C-terminus of the B-chain of insulin behaves as a zipper and exhibits transitions between closed (inactive) to a wide-open (active) conformer to facilitate binding to IR. The conformational transitions, key residues, and the energetics of BC-CT were investigated using MD simulations ( 95 , 100 , 108 ). To probe the effect of varying pressure, temperature, pH, chemical modifications, and electric field on the structure of insulin, several MD studies were conducted ( 71 , 78 , 79 , 84 , 102 , 122 ).…”

“…They concluded that insulin strongly interacts with the nanosheets by its flexible C- and N-termini. The probability density function and the potential of mean force calculations were performed to understand the effects of mutations on the dynamics of the BC-CT opening and the energetics of insulin activation ( 108 ). Several studies revealed that BC-CT unzips from the hydrophobic core to facilitate binding of insulin to IR ( 40 , 95 , 165 – 167 ).…”

Mapping Structural Drivers of Insulin Analogs Using Molecular Dynamics and Free Energy Calculations at Insulin Receptor

“…[1][2][3] Mature bioactive human insulin has been structurally well-characterized and is a 51 amino acid peptide consisting of two chains A and B held together by two inter-chain disulfide bridges and further stabilised by an intra-chain-A cysteine-bridge. [4][5][6][7][8] Insulin mediates a host of important metabolic functions through its engagement with the insulin receptor (IR). 1,4,9,10 The IR belongs to the receptor tyrosine kinase (RTK) family of receptors that include type 1 and 2 insulin like growth factor receptors (IGF1-and IGF-2R) and the orphan insulin receptor-related receptor.…”

“…4 These structures were complemented by computational studies that emphasised the importance of these domains for insulin binding. 6,7,[13][14][15] In 2018, single electron microscopy (EM) experiments have shown that activation of the insulin-IR complex involved transitioning from an inverted 'V' conformation to a T-like state that is thought to allow the transmembrane domains to come in proximity to each other and result in auto-phosphorylation and downstream signaling. 2 In the same year, Xu et al, resolved the structure of the IGF-1R bound to its cognate ligand the insulin-like growth factor (IGF), which revealed both similarities and differences with the IR-insulin complex.…”

“…15,17,18 Abnormalities in insulin secretion or resistance to insulin leads to type-1 or 2 diabetes. 15,[18][19][20][21] Monomeric insulin mediates a host of important functions primarily through its engagement with the IR. 1,18,22,23 The IR belongs to the receptor tyrosine kinase (RTK) family of proteins that include type 1 and 2 insulin like growth factor receptors (IGF1-and IGF-2R) and the orphan insulin receptor-related receptor.…”