Binding modes of Bcl-2 homology 3 (BH3) peptides with anti-apoptotic protein A1 and redesign of peptide inhibitors: a computational study

In-silico identification of potential peptide inhibitors to disrupt NLRP3 inflammasome complex formation by blocking NLRP3-ASC pyrin-pyrin interactions

The NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome is a well-known and frequently cited regulator of caspase-1 activation. It plays a significant role in several pathophysiological processes and is a major regulator of the innate immune response. A growing amount of scientific evidences for its aberrant activation in various chronic inflammatory diseases attracts a growing interest in the development of new NLRP3 inhibitors. One of the successful strategies used to identify new inhibitors is peptide inhibitors. Compared to small molecule inhibitors, peptide inhibitors show greater selectivity and less toxicity. In this study, we used an in-silico mutagenesis approach to design new peptide inhibitors from reported peptide inhibitor of NLRP3. The sequence of the peptide inhibitor against NLRP3 was searched from the literature and modeled using the online server PEP-FOLD3. The in-silico alanine scanning mutagenesis of the reference peptide revealed that residues, Y23, R28, E6, I26, R20, L19, Q33, K11, L14, and K13 have positive affinity values and are therefore better candidates for substitution to increase binding affinity. By replacing these residues, the affinity of the newly designed peptide inhibitors for the NLRP3 PYD protein was significantly increased. Further, molecular dynamics simulations and binding energy calculations validated the stability and higher binding affinities of the newly designed peptide inhibitors compared to the wild-type peptide inhibitor. Our research revealed that all the suggested peptide inhibitors have higher binding affinities for the NLRP3 protein as compared to the native wild-type peptide inhibitor and could block NLRP3-ASC pyrin-pyrin interaction.

Molecular Insights into the Improved Bioactivity of Interferon Conjugates Attached to a Helical Polyglutamate

Attaching polymers, especially polyethylene glycol (PEG), to protein drugs has emerged as a successful strategy to prolong circulation time in the bloodstream. The hypothesis is that the flexible chain wobbles on the protein's surface, thus resisting potential nonspecific adsorption. Such a theoretical framework may be challenged when a helical polyglutamate is used to conjugate with target proteins. In this study, we investigated the structure-activity relationships of polyglutamate-interferon conjugates P(EG₃Glu)-IFN using molecular simulations. Our results show that the local crowding effect induced by oligoethylene glycols (i.e., EG₃) is the primary driving force for helix formation in P(EG₃Glu), and its helicity can be effectively increased by reducing the free volume of the two termini. Furthermore, it was found that the steric hindrance induced by IFN is not conductive to the helicity of P(EG₃Glu) but contributes to its dominant orientation relative to interferon. The orientation of IFN relative to the helical P(EG₃Glu) can help to protect the protein drug from neutralizing antibodies while maintaining its bioactivity. These findings suggest that the helical structure and its orientation are critical factors to consider when updating the theoretical framework for protein-polymer conjugates.

Sequence Effect of Peptide-Based Materials on Delivering Interferon-α (IFN-α): A Molecular Dynamic Perspective

Peptide-based biomaterials exhibit great potentials in developing drug delivery platforms due to their biocompatibility and biodegradability beyond poly(ethylene glycol). How different amino acids in peptides used for delivery play their roles is still unclear at the microscopic level. This work compared the assembly behaviors of a series of peptides around interferon-α (IFN-α). Through all-atom molecular simulations, the sequence effect of peptides on delivering interferon-α was quantitively characterized. The hydrophobic elastin-like peptide (VPGAG)_n preferred to self-aggregate into dense clusters, rather than encapsulate IFN-α. The hydrophilic zwitterionic peptides with repeating unit "KE" tended to phase-separate from IFN-α in the mixture. In contrast, peptides with a hybrid sequence, i.e., (VPKEG)_n, exhibited the highest contact preference, and the formed protective shell endowed IFN-α with better thermal stability and stealth property and achieved a subtle balance between protecting IFN-α and subsequent releasing. Further energy decomposition analysis revealed that the positively charged Lys contributed most to the binding affinity while the negatively charged Glu contributed most to the hydrophilic property of peptide-based materials. In summary, this article reveals why peptides composed of repeating hydrophobic and charged residues could be a potential choice for delivering therapeutic proteins in the form of solution.

Apoptosis and its therapeutic implications in neurodegenerative diseases

Neurodegenerative disorders are characterized by progressive loss of particular populations of neurons. Apoptosis has been implicated in the pathogenesis of neurodegenerative diseases, including Parkinson disease, Alzheimer disease, Huntington disease, and amyotrophic lateral sclerosis. In this review, we focus on the existing notions relevant to comprehending the apoptotic death process, including the morphological features, mediators and regulators of cellular apoptosis. We also highlight the evidence of neuronal apoptotic death in Parkinson disease, Alzheimer disease, Huntington disease, and amyotrophic lateral sclerosis. Additionally, we present evidence of potential therapeutic agents that could modify the apoptotic pathway in the aforementioned neurodegenerative diseases and delay disease progression. Finally, we review the clinical trials that were conducted to evaluate the use of anti-apoptotic drugs in the treatment of the aforementioned neurodegenerative diseases, in order to highlight the essential need for early detection and intervention of neurodegenerative diseases in humans.

Inhibition of Anti-Apoptotic Bcl-2 Proteins in Preclinical and Clinical Studies: Current Overview in Cancer

The dynamic interplay between pro-death and pro-survival Bcl-2 family proteins is responsible for a cell’s fate. Due to the recognized relevance of this family in cancer progression and response to therapy, different efforts have made in recent years in order to develop small molecules able to target anti-apoptotic proteins such as Bcl-2, Bcl-xL and Mcl-1. The limitations of the first Bcl-2 family targeted drugs, regarding on-target and off-target toxicities, have been overcome with the development of venetoclax (ABT-199), the first BH3 mimetic inhibitor approved by the FDA. The purpose of this review is to discuss the state-of-the-art in the development of drugs targeting Bcl-2 anti-apoptotic proteins and to highlight the potential of their application as single agents or in combination for improving anti-cancer therapy, focusing in particular on solid tumors.

Biomimetic Design of Peptide Neutralizer of Ebola Virus with Molecular Simulation

Ebola virus (EBOV) belongs to the Filoviridae family, which can cause severe hemorrhagic fever in humans and nonprimates. The neutralization of EBOV by monoclonal antibody (mAb) ADI-15946 was reported recently. In the present study, the molecular interactions between the receptor GPcl of EBOV and ADI-15946 were studied by molecular dynamics (MD) simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis. Hydrophobic interaction was identified as the main driving force for the binding of ADI-15946 on EBOV. Moreover, the contribution of each amino acid residue for the binding was evaluated. Then, an affinity binding model (ABM) was constructed using the residues favorable for the binding, including Y107, F108, D109, W110, and R113. The biomimetic design of neutralizer against EBOV according to the ABM of ADI-15946 was then performed, followed by screening using docking, structural similarity. Two neutralizers YFDWHMR and YFDWRYR were obtained, which were proven to be capable of strong binding on GPcl and then neutralizing GPcl. These results would be helpful for the development of neutralizers for Ebola virus.

Targeting cancer's Achilles’ heel: role of BCL-2 inhibitors in cellular senescence and apoptosis

Members of the antiapoptotic BCL-2 proteins are involved in tumor growth, progression and survival, and are also responsible for chemoresistance to conventional anticancer agents. Early efforts to target these proteins yielded some active compounds; however, newer methodologies involving structure-based drug design, Nuclear Magnetic Resonance (NMR)-based screening and fragment-based screening yielded more potent compounds. Discovery of specific as well as nonspecific inhibitors of this class of proteins has resulted in great advances in targeted chemotherapy and decrease in chemoresistance. Here, we review the history and current progress in direct as well as selective targeting of the BCL-2 proteins for anticancer therapy.

Structural-dynamic insights into the H. pylori cytotoxin-associated gene A (CagA) and its abrogation to interact with the tumor suppressor protein ASPP2 using decoy peptides

Helicobacter pylori (H. pylori) is one of the most extensively studied Gram-negative bacteria due to its implication in gastric cancer. The oncogenicity of H. pylori is associated with cytotoxin-associated gene A (CagA), which is injected into epithelial cells lining the stomach. Both the C- and N-termini of CagA are involved in the interaction with several host proteins, thereby disrupting vital cellular functions, such as cell adhesion, cell cycle, intracellular signal transduction, and cytoskeletal structure. The N-terminus of CagA interacts with the tumor-suppressing protein, apoptosis-stimulating protein of p53 (ASPP2), subsequently disrupting the apoptotic function of tumor suppressor gene p53. Here, we present the in-depth molecular dynamic mechanism of the CagA-ASPP2 interaction and highlight hot-spot residues through in silico mutagenesis. Our findings are in agreement with previous studies and further suggest other residues that are crucial for the CagA-ASPP2 interaction. Furthermore, the ASPP2-binding pocket possesses potential druggability and could be engaged by decoy peptides, identified through a machine-learning system and suggested in this study. The binding affinities of these peptides with CagA were monitored through extensive computational procedures and reported herein. While CagA is crucial for the oncogenicity of H. pylori, our designed peptides possess the potential to inhibit CagA and restore the tumor suppressor function of ASPP2.