Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation

The binding pattern of ferric iron and iron-binding protein in Botrytis cinerea

Iron-binding protein (Ibp) has protective effect on pathogen exposed to H2O2 in defense response of plants. Ibp in Botrytis cinerea (BcIbp) is related to its virulence. Bcibp mutation lead to virulence deficiencies in B. cinerea. BcIbp is involved in the Fe3+ homeostasis regulation. Recognition the binding site and binding pattern of ferric iron and iron-binding protein in B. cinerea are vital to understand its function. In this study, molecular dynamics (MD) simulations, gaussian accelerated molecular dynamics (GaMD) simulations, dynamic cross correlation analysis and quantum chemical energy calculation were used to explore binding pattern of ferric iron. MD results showed that the C-terminal region had little effect on the stability of residues in the Fe3+-binding pocket. Energy calculations suggested the most likely coordination pattern for ferric iron in iron-binding protein. These results will help to understand the binding of ferric iron to iron-binding protein and provide new ideas for regulating the virulence of B. cinerea.

Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics

The HRAS protein is considered a critical target for drug development in cancers. It is vital for effective drug development to understand the effects of mutations on the binding of GTP and GDP to HRAS. We conducted Gaussian accelerated molecular dynamics (GaMD) simulations and free energy landscape (FEL) calculations to investigate the impacts of two mutations (A59E and K117R) on GTP and GDP binding and the conformational states of the switch domain. Our findings demonstrate that these mutations not only modify the flexibility of the switch domains, but also affect the correlated motions of these domains. Furthermore, the mutations significantly disrupt the dynamic behavior of the switch domains, leading to a conformational change in HRAS. Additionally, these mutations significantly impact the switch domain's interactions, including their hydrogen bonding with ligands and electrostatic interactions with magnesium ions. Since the switch domains are crucial for the binding of HRAS to effectors, any alterations in their interactions or conformational states will undoubtedly disrupt the activity of HRAS. This research provides valuable information for the design of drugs targeting HRAS.

Identification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling

Kirsten rat sarcoma viral oncogene homolog (KRas) activating mutations are common in solid tumors, accounting for 90%, 45%, and 35% of pancreatic, colorectal, and lung cancers (LC), respectively. Each year, nearly 150k new cases (both men and women) of KRas-mutated malignancies are reported in the United States. NSCLC (non-small cell lung cancer) accounts for 80% of all LC cases. KRas mutations are found in 15% to 25% of NSCLC patients. The main cause of NSCLC is the KRas-G12C mutation. The drugs Sotorasib and Adagrasib were recently developed to treat advanced NSCLC caused by the KRas-G12C mutation. Most patients do not respond to KRas-G12C inhibitors due to cellular, molecular, and genetic resistance. Because of their safety, efficacy, and selectivity, peptide inhibitors have the potential to treat newly developing KRas mutations. Based on the KRas mutations, peptide inhibitors that are highly selective and specific to individual lung cancers can be rationally designed. The current study uses an alanine and residue scanning approach to design peptide inhibitors for KRas-G12C based on the known peptide. Our findings show that substitution of F3K, G11T, L8C, T14C, K13D, G11S, and G11P considerably enhances the binding affinity of the novel peptides, whereas F3K, G11T, L8C, and T14C peptides have higher stability and favorable binding to the altered peptides. Overall, our study paves the road for the development of potential therapeutic peptidomimetics that target the KRas-G12C complex and may inhibit the KRas and SOS complex from interacting.Communicated by Ramaswamy H. Sarma.

An In Silico Design of Peptides Targeting the S1/S2 Cleavage Site of the SARS-CoV-2 Spike Protein

SARS-CoV-2, responsible for the COVID-19 pandemic, invades host cells via its spike protein, which includes critical binding regions, such as the receptor-binding domain (RBD), the S1/S2 cleavage site, the S2 cleavage site, and heptad-repeat (HR) sections. Peptides targeting the RBD and HR1 inhibit binding to host ACE2 receptors and the formation of the fusion core. Other peptides target proteases, such as TMPRSS2 and cathepsin L, to prevent the cleavage of the S protein. However, research has largely ignored peptides targeting the S1/S2 cleavage site. In this study, bioinformatics was used to investigate the binding of the S1/S2 cleavage site to host proteases, including furin, trypsin, TMPRSS2, matriptase, cathepsin B, and cathepsin L. Peptides targeting the S1/S2 site were designed by identifying binding residues. Peptides were docked to the S1/S2 site using HADDOCK (High-Ambiguity-Driven protein-protein DOCKing). Nine peptides with the lowest HADDOCK scores and strong binding affinities were selected, which was followed by molecular dynamics simulations (MDSs) for further investigation. Among these peptides, BR582 and BR599 stand out. They exhibited relatively high interaction energies with the S protein at -1004.769 ± 21.2 kJ/mol and -1040.334 ± 24.1 kJ/mol, respectively. It is noteworthy that the binding of these peptides to the S protein remained stable during the MDSs. In conclusion, this research highlights the potential of peptides targeting the S1/S2 cleavage site as a means to prevent SARS-CoV-2 from entering cells, and contributes to the development of therapeutic interventions against COVID-19.

Computational investigation on the effect of the lysine 2-hydroxyisobutyrylation on argininosuccinate synthetase 1 conformational dynamics in Botrytis cinerea

Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in recent years, which has been identified in several species and is associated with diverse cellular functions. Botrytis cinerea, as a broad host pathogen, is very destructive and causes serious losses to agricultural economy. Argininosuccinate synthetase (ASS, citrulline-aspartate ligase) is the rate-limiting enzyme in the catalytic arginine synthesis pathway. Arginine deficiency can affect the growth of Botrytis cinerea. The Khib site Lys120 was found in functional domain of argininosuccinate synthetase 1 from Botrytis cinerea (Bcass1), which is located in conserved loop. It is worth exploring how K120hib affects the conformation of Bcass1. In this study, molecular dynamics (MD) simulations, binding free energy calculation, principal component analysis (PCA), and dynamic cross-correlation analysis were used to explore the influence of K120hib on the conformation of Bcass1. The increase of root-mean-square fluctuation (RMSF) value of related residues and PCA results suggests that K120hib increases the flexibility of some regions of Bcass1. Moreover, K120hib weakens the binding free energy between Bcass1 and the two substrates. These results will help to understand the effects of K120hib on Bcass1 and provide new ideas for regulating the pathogenicity of Botrytis cinerea.

In Silico Study of the Acquired Resistance Caused by the Secondary Mutations of KRAS G12C Protein Using Long Time Molecular Dynamics Simulation and Markov State Model Analysis

Kirsten rat sarcoma viral oncogene homolog (KRAS) is a small GTPase protein which plays an important role in the treatment of KRAS mutant cancers. The FDA-approved AMG510 and MRTX849 (phase III clinical trials) are two potent KRASG12C-selective inhibitors that target KRAS G12C. However, the drug resistance caused by the second-site mutation in KRAS has emerged, and the mechanisms of drug resistance at atom level are still unclear. To clarify the mechanisms of drug resistance, we conducted long time molecular dynamics simulations (75 μs in total) to study the structural and energetic features of KRAS G12C and its four drug resistant variants to inhibitors. The combined binding free energy calculation and protein-ligand interaction fingerprint revealed that these second-site mutations indeed caused KRAS to produce different degrees of resistance to AMG510 and MRTX849. Furthermore, Markov State Models and 2D-free energy landscapes analysis revealed the difference in conformational changes of mutated KRAS bound with and without inhibitors. Furthermore, the comparative analysis of these systems showed that there were differences in their allosteric signal pathways. These findings provide the molecular mechanism of drug resistance, which helps to guide novel KRAS G12C inhibitor design to overcome drug resistance.

Computer-Aided Drug Design Boosts RAS Inhibitor Discovery

The Rat Sarcoma (RAS) family (NRAS, HRAS, and KRAS) is endowed with GTPase activity to regulate various signaling pathways in ubiquitous animal cells. As proto-oncogenes, RAS mutations can maintain activation, leading to the growth and proliferation of abnormal cells and the development of a variety of human cancers. For the fight against tumors, the discovery of RAS-targeted drugs is of high significance. On the one hand, the structural properties of the RAS protein make it difficult to find inhibitors specifically targeted to it. On the other hand, targeting other molecules in the RAS signaling pathway often leads to severe tissue toxicities due to the lack of disease specificity. However, computer-aided drug design (CADD) can help solve the above problems. As an interdisciplinary approach that combines computational biology with medicinal chemistry, CADD has brought a variety of advances and numerous benefits to drug design, such as the rapid identification of new targets and discovery of new drugs. Based on an overview of RAS features and the history of inhibitor discovery, this review provides insight into the application of mainstream CADD methods to RAS drug design.

Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect

The Ras-specific guanine nucleotide exchange factors Son of Sevenless (SOS) regulates Ras activation by converting inactive GDP-bound to active GTP-bound states. The catalytic activity of Ras is further allosterically regulated by GTP−Ras bound to a distal site through a positive feedback loop. To address the mechanism underlying the long-range allosteric activation of the catalytic K-Ras4B by an additional allosteric GTP–Ras through SOS, we employed molecular dynamics simulation of the K-Ras4B^G13D•SOS^cat complex with and without an allosteric GTP-bound K-Ras4B^G13D. We found that the binding of an allosteric GTP−K-Ras4B^G13D enhanced the affinity between the catalytic K-Ras4B^G13D and SOS^cat, forming a more stable conformational state. The peeling away of the switch I from the nucleotide binding site facilitated the dissociation of GDP, thereby contributing to the increased nucleotide exchange rate. The community networks further showed stronger edge connection upon allosteric GTP−K-Ras4B^G13D binding, which represented an increased interaction between catalytic K-Ras4B^G13D and SOS^cat. Moreover, GTP−K-Ras4B^G13D binding transmitted allosteric signaling pathways though the Cdc25 domain of SOS that enhanced the allosteric regulatory from the K-Ras4B^G13D allosteric site to the catalytic site. This study may provide an in-depth mechanism for abnormal activation and allosteric regulation of K-Ras4B^G13D.

Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A

An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-CDNAJB1) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-CDNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera's allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-CDNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.

Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics

Uncovering molecular basis with regard to the conformational change of two switches I and II in the GppNHp (GNP)-bound H-Ras is highly significant for the understanding of Ras signaling. For this purpose, accelerated molecular dynamics (aMD) simulations and principal component (PC) analysis are integrated to probe the effect of mutations G12V, T35S and Q61K on conformational transformation between two switches of the GNP-bound H-Ras. The RMSF and cross-correlation analyses suggest that three mutations exert a vital effect on the flexibility and internal dynamics of two switches in the GNP-bound H-Ras. The results stemming from PC analysis indicate that two switches in the GNP-bound WT H-Ras tend to form a closed state in most conformations, while those in the GNP-bound mutated H-Ras display transformation between different states. This conclusion is further supported by free energy landscapes constructed by using the distances of residues 12 away from 35 and 35 away from 61 as reaction coordinates and different experimental studies. Interaction scanning is performed on aMD trajectories and the information shows that conformational transformations of two switches I and II induced by mutations extremely affect the GNP-residue interactions. Meanwhile, the scanning results also signify that residues G15, A18, F28, K117, A146 and K147 form stable contacts with GNP, while residues D30, E31, Y32, D33, P34 and E62 in two switches I and II produce unstable contacts with GNP. This study not only reveals dynamic behavior changes of two switches in H-Ras induced by mutations, but also unveils general principles and mechanisms with regard to functional conformational changes of H-Ras.

How Parkinson's disease-related mutations disrupt the dimerization of WD40 domain in LRRK2: a comparative molecular dynamics simulation study

The multidomain kinase enzyme leucine-rich-repeat kinase 2 (LRRK2), activated through a homodimerization manner, has been identified as an important pathogenic factor in Parkinson's disease (PD), the second most common neurodegenerative disease wordwide. The Trp-Asp-40 (WD40) domain, located in the C-terminal LRRK2, harbours one of the most frequent PD-related variants, G2385R. However, the detailed dynamics of WD40 during LRRK2 dimerization and the underlying mechanism through which the pathogenic mutations disrupt the formation of the WD40 dimer have remained elusive. Here, microsecond-scale molecular dynamics simulations were employed to provide a mechanistic view underlying the WD40 dimerization and unveil the structural basis by which the interface-based mutations G2385R, H2391D and R2394E compromise the corresponding process. The simulation results identified important residues, D2351, R2394, E2395, R2413, and R2443, involved in establishing the complex binding network along the dimerization interface, which was significantly weakened in the presence of interfacial mutations. A "sag-bulge" model was proposed to explain the unfavorable dimer formation in the mutant systems. In addition, mutations altered the community configuration in the wild-type system in which inter-monomeric interplay is prominent, leading to the destabilization of the WD40 dimer under mutation.

Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B

Ras is a key member in the superfamily of small GTPase. Transforming between GTP-bound active state and GDP-bound inactive state in response to exogenous signals, Ras serves as a binary switch in various signaling pathways. One of its downstream effectors is phosphatidylinositol-4,5-bisphosphate 3-kinase α (PI3Kα), which phosphorylates phosphatidylinositol 4,5-bisphosphate into phosphatidylinositol 3,4,5-trisphosphate in the PI3K/Akt/mTOR pathway and mediates an array of important cellular activities including cell growth, migration and survival. Hyperactivation of PI3Kα induced by the Ras isoform K-Ras4B has been unveiled as a key event during the oncogenesis of pancreatic ductal adenocarcinoma, but the underlying mechanism of how K-Ras4B allosterically activates PI3Kα still remains largely unsolved. Here, we employed accelerated molecular dynamic simulations and allosteric pathway analysis to explore into the activation process of PI3Kα by K-Ras4B and unraveled the underlying structural mechanisms. We found that K-Ras4B binding induced more conformational dynamics within PI3Kα and triggered its step-wise transition from a self-inhibited state towards an activated state. Moreover, K-Ras4B binding markedly disrupted the interactions along the p110/p85 interface, especially the ones between nSH2 in p85 and its nearby functional domains in p110 like C2, helical, and kinase domains. The altered inter-domain interactions exposed the kinase domain, which promoted the membrane association and substrate phosphorylation of PI3Kα, thereby facilitating its activation. In particular, the community networks and allosteric pathways analysis further revealed that in PI3Kα/K-Ras4B system, allosteric signaling regulating p110/p85 interaction was rewired from the helical domain to the kinase domain and several important residues and their related allosteric pathways mediating PI3Kα autoinhibition were bypassed. The obtained structural mechanisms provide an in-depth mechanistic insight into the allosteric activation of PI3Kα by K-Ras4B as well as shed light on its drug discovery.

The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1

Phosphoinositide-dependent protein kinase-1 (PDK1) is an important protein in mediating the PI3K-AKT pathway and is thus identified as a promising target. The catalytic activity of PDK1 is tightly regulated by allosteric modulators, which bind to the PDK1 Interacting Fragment (PIF) pocket of the kinase domain that is topographically distinct from the orthosteric, ATP binding site. Allosteric modulators by attaching to the less conserved PIF-pocket have remarkable advantages such as higher selectivity, less side effect, and lower toxicity. Targeting allosteric PIF-pocket of PDK1 has become the focus of recent attention. In this review, we summarise the current advances in the structure-based discovery of PDK1 allosteric modulators. We will first present the three-dimensional structure of PDK1 and illustrate the allosteric regulatory mechanism of PDK1 through the modulation of the PIF-pocket. Then, the recent advances of PDK1 allosteric modulators targeting the PIF-pocket will be recapitulated detailly according to the structural similarity of allosteric modulators.

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Drugging K-RasG12C through covalent inhibitors: Mission possible?

Ras, whose mutants are present in approximately 30% of human tumours, is one of the most important oncogenes. Drugging Ras is thus regarded as the quest for the Holy Grail in cancer therapeutics development. Despite more than three decades of efforts, drug discovery targeting Ras constantly fails, rendering Ras undruggable, due to its smooth surface and picomolar affinity towards guanosine substrates. The most frequently mutated isoform of Ras is K-Ras, accounting for >85% of Ras-driven cancers, and one majority of them is the G12C mutation. Recent advances in structural biology shed light on drugging Ras, and one of the cutting-edge breakthroughs is the design of covalent G12C-specific inhibitors targeting the mutated cysteine. This type of inhibitor can be classified into substrate-competitive orthosteric inhibitors and non-competitive allosteric inhibitors. They display improved selectivity and enhanced potency due to their G12-specific and irreversible covalent binding nature. Thus, they represent a new hope for revolutionizing the conventional characterization of Ras as "undruggable" and pave a promising avenue for further drug discovery. Here, we provide comprehensive structural and medicinal chemical insights into K-Ras covalent inhibitors specific for the G12C mutant. We first present an in-depth analysis of the conformations of the inhibitor binding pockets. Then, all the latest covalent ligands selectively inhibiting K-Ras^G12C are reviewed. Finally, we examine the current challenges faced by this new class of anti-Ras inhibitors.

The structural basis of the autoinhibition mechanism of glycogen synthase kinase 3β (GSK3β): molecular modeling and molecular dynamics simulation studies

The autoinhibition phenomenon has been frequently observed in enzymes and represents an important regulatory strategy to fine-tune enzyme activity. Evolution has exploited this mechanism to reduce enzymatic activity. Glycogen synthase kinase 3β (GSK3β) undergoes autoinhibition via the phosphorylation of Ser9 at the N-terminus of the kinase, which, acting as a pseudosubstrate, occupies the catalytic domain of GSK3β and subsequently blocks primed substrates from having access to the catalytic domain. The detailed structural basis of the autoinhibition mechanism of GSK3β by the pseudosubstrate, however, has not yet been fully resolved. Here, a three-dimensional model of the binary GSK3β-pseudosubstrate complex was built via the molecular modeling method. Based on the constructed model, extensive molecular dynamics (MD) simulations and subsequent molecular mechanics generalized Born/surface area (MM_GBSA) calculations were performed on the wild-type GSK3β-pseudosubstrate complex and three mutated systems (R4A, R6A, and S9A). Analyses of MD simulations and binding free energies revealed that the phosphorylation of Ser9 is the prerequisite for the autoinhibition of GSK3β, and both mutations of Arg4 and Arg6 to alanine markedly reduced the binding affinities of the mutated pseudosubstrate to the GSK3β catalytic domain, thereby disrupting the autoinhibition of the kinase. This study highlights the importance of Ser9, Arg6, and Arg4 in modulating the autoinhibition mechanism of GSK3β, contributing to a deeper understanding of GSK3β biology.Communicated by Ramaswamy H. Sarma.

Computational Insights into the Interactions between Calmodulin and the c/nSH2 Domains of p85α Regulatory Subunit of PI3Kα: Implication for PI3Kα Activation by Calmodulin

Calmodulin (CaM) and phosphatidylinositide-3 kinase (PI3Kα) are well known for their multiple roles in a series of intracellular signaling pathways and in the progression of several human cancers. Crosstalk between CaM and PI3Kα has been an area of intensive research. Recent experiments have shown that in adenocarcinoma, K-Ras4B is involved in the CaM-PI3Kα crosstalk. Based on experimental results, we have recently put forward a hypothesis that the coordination of CaM and PI3Kα with K-Ras4B forms a CaM-PI3Kα-K-Ras4B ternary complex, which leads to the formation of pancreatic ductal adenocarcinoma. However, the mechanism for the CaM-PI3Kα crosstalk is unresolved. Based on molecular modeling and molecular dynamics simulations, here we explored the potential interactions between CaM and the c/nSH2 domains of p85α subunit of PI3Kα. We demonstrated that CaM can interact with the c/nSH2 domains and the interaction details were unraveled. Moreover, the possible modes for the CaM-cSH2 and CaM-nSH2 interactions were uncovered and we used them to construct a complete CaM-PI3Kα complex model. The structural model of CaM-PI3Kα interaction not only offers a support for our previous ternary complex hypothesis, but also is useful for drug design targeted at CaM-PI3Kα protein-protein interactions.