Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes.

The phenomenon of protein aggregation is associated with a wide range of human diseases. Our knowledge of the aggregation behaviour of viral proteins, however, is still rather limited. Here, we investigated this behaviour in the SARS-CoV and SARS-CoV-2 proteomes. An initial analysis using a panel of sequence-based predictors suggested the presence of multiple aggregation-prone regions (APRs) in these proteomes and revealed a strong aggregation propensity in some SARS-CoV-2 proteins. We then studied the in vitro aggregation of predicted aggregation-prone SARS-CoV and SARS-CoV-2 proteins and protein regions, including the signal sequence peptide and fusion peptides 1 and 2 of the spike protein, a peptide from the NSP6 protein, and the ORF10 and NSP11 proteins. Our results show that these peptides and proteins can form amyloid aggregates. We used circular dichroism spectroscopy to reveal the presence of ß-sheet rich cores in aggregates and X-ray diffraction and Raman spectroscopy to confirm the formation of amyloid structures. Furthermore, we demonstrated that SARS-CoV-2 NSP11 aggregates are toxic to mammalian cell cultures. These results motivate further studies about the possible role of aggregation of SARS proteins in protein misfolding diseases and other human conditions.

Substituent-Controlled Structural, Supramolecular, and Cytotoxic Properties of a Series of 2-Styryl-8-nitro and 2-Styryl-8-hydroxy Quinolines.

Styryl quinolines are biologically active compounds with properties largely depending on the substituents on the styryl and quinoline rings. The supramolecular aspects of this class of compounds are rarely explored. In this study, two new series of styryl quinoline derivatives, bearing -OH and -NO2 groups at the eighthposition of the quinoline ring and -SCH3, -OCH3, and -Br groups on the styryl ring, have been developed, and their structural, supramolecular, and cytotoxic properties have been analyzed. Crystallographic analyses revealed the exciting substituent-dependent structural and supramolecular features of these compounds. In general, the 8 -OH substituted derivatives (SA series) exhibited a non-planar molecular geometry having larger dihedral angles (5.75-59.3°) between the planes of the aromatic rings. At the same time, the 8 -NO2 substituted derivatives (SB series) exhibited a more or less planar molecular geometry, as revealed by the smaller dihedral angles (1.32-3.45°) between the aromatic rings. Multiple O-H···O, C-H···O, O-H···N, and π-π stacking interactions among the molecules lead to fascinating supramolecular architectures such as hydrogen-bonded triple helices, zig-zag 1D chains, π-π stacked infinite chains, and so forth in their crystal lattice. Hirshfeld surface analyses confirmed the existence of strong π-π stacking and other weak bonding interactions in these compounds. The preliminary cytotoxic properties of SA and SB series compounds were evaluated against the human cervical cancer cell lines (HeLa cells), which further highlighted the roles of functional substituents on the aromatic rings. The SA series compounds with the -OH substituent on the quinoline ring exhibited better cytotoxicity than the SB series compounds with a -NO2 substituent. Similarly, the electron-withdrawing group -Br on the styryl ring enhanced the cytotoxicity in both series. The IC50 values were 2.52-4.69 and 2.897-10.37 µM, respectively, for the SA and SB series compounds. Compound S3A having -OH and -Br groups on the quinoline and styryl ring, respectively, exhibited the best IC50 value of 2.52 µM among all the compounds tested. These findings confirm the relevance of the hydroxyl group in the eighth position of quinoline. In short, the present study attempts to provide a systematic analysis of the effects of aromatic ring substituents on the structural, supramolecular, and cytotoxic properties of styryl quinolines for the first time.

Role of structural disorder in the multi-functionality of flavivirus proteins.

INTRODUCTION: The life cycle of a virus involves interacting with the host cell, entry, hijacking host machinery for viral replication, evading the host's immune system, and releasing mature virions. However, viruses, being small in size, can only harbor a genome large enough to code for the minimal number of proteins required for the replication and maturation of the virions. As a result, many viral proteins are multifunctional machines that do not directly obey the classic structure-function paradigm. Often, such multifunctionality is rooted in intrinsic disorder that allows viral proteins to interact with various cellular factors and remain functional in the hostile environment of different cellular compartments. AREAS COVERED: This report covers the classification of flaviviruses, their proteome organization, and the prevalence of intrinsic disorder in the proteomes of different flaviviruses. Further, we have summarized the speculations made about the apparent roles of intrinsic disorder in the observed multifunctionality of flaviviral proteins. EXPERT OPINION: Small sizes of viral genomes impose multifunctionality on their proteins, which is dependent on the excessive usage of intrinsic disorder. In fact, intrinsic disorder serves as a universal functional tool, weapon, and armor of viruses and clearly plays an important role in their functionality and evolution.

Functional inhibition of c-Myc using novel inhibitors identified through "hot spot" targeting.

Protein-protein interactions drive various biological processes in healthy as well as disease states. The transcription factor c-Myc plays a crucial role in maintaining cellular homeostasis, and its deregulated expression is linked to various human cancers; therefore, it can be considered a viable target for cancer therapeutics. However, the structural heterogeneity of c-Myc due to its disordered nature poses a major challenge to drug discovery. In the present study, we used an in silico alanine scanning mutagenesis approach to identify "hot spot" residues within the c-Myc/Myc-associated factor X interface, which is highly disordered and has not yet been systematically analyzed for potential small molecule binding sites. We then used the information gained from this analysis to screen potential inhibitors using a conformation ensemble approach. The fluorescence-based biophysical experiments showed that the identified hit molecules displayed noncovalent interactions with these hot spot residues, and further cell-based experiments showed substantial in vitro potency against diverse c-Myc-expressing cancer/stem cells by deregulating c-Myc activity. These biophysical and computational studies demonstrated stable binding of the hit compounds with the disordered c-Myc protein. Collectively, our data indicated effective drug targeting of the disordered c-Myc protein via the determination of hot spot residues in the c-Myc/Myc-associated factor X heterodimer.

Advancement of Single-Cell Sequencing in Medulloblastoma.

Single-cell sequencing is a promising attempt to investigate the genomic, transcriptomic, and multiomic level of individual cell in the larger population of cells. The outward evolution of the technique from a manual method to the automation of single-cell sequencing is cogent. Lately, single-cell sequencing is widely used in various fields of science and has applications in neurobiology, immunity, cancer, microbiology, reproduction, and digestion. This chapter introduces the reader to the details of single-cell sequencing, currently used in several small-scale and commercial platforms. The advancement of single-cell sequencing in brain cancer sheds light on questions unanswered so far in the field of oncology.

A novel inhibitor L755507 efficiently blocks c-Myc-MAX heterodimerization and induces apoptosis in cancer cells.

c-Myc is a transcription factor that plays a crucial role in cellular homeostasis, and its deregulation is associated with highly aggressive and chemotherapy-resistant cancers. After binding with partner MAX, the c-Myc-MAX heterodimer regulates the expression of several genes, leading to an oncogenic phenotype. Although considered a crucial therapeutic target, no clinically approved c-Myc-targeted therapy has yet been discovered. Here, we report the discovery via computer-aided drug discovery of a small molecule, L755507, which functions as a c-Myc inhibitor to efficiently restrict the growth of diverse Myc-expressing cells with low micromolar IC50 values. L755507 successfully disrupts the c-Myc-MAX heterodimer, resulting in decreased expression of c-Myc target genes. Spectroscopic and computational experiments demonstrated that L755507 binds to the c-Myc peptide and thereby stabilizes the helix-loop-helix conformation of the c-Myc transcription factor. Taken together, this study suggests that L755507 effectively inhibits the c-Myc-MAX heterodimerization and may be used for further optimization to develop a c-Myc-targeted antineoplastic drug.

Microbiome and host crosstalk: A new paradigm to cancer therapy.

The commensal microbiome of humans has co-evolved for thousands of years. The microbiome regulates human health and is also linked to several diseases, including cancer. The advances in next-generation sequencing have significantly contributed to our understanding of the microbiome and its association with cancer and cancer therapy. Recent studies have highlighted a close relationship of the microbiome to the pharmacological effect of chemotherapy and immunotherapy. The chemo-drugs usually interfere with the host immune system and reduces the microbiome diversity inside the body, which in turn leads to decreased efficacy of these drugs. The human microbiome, specifically the gut microbiome, increases the potency of chemo-drugs through metabolism, enzymatic degradation, ecological differences, and immunomodulation. Recent research exploits the involvement of microbiome to shape the efficacy and decrease the toxicity of these chemo-drugs. In this review, we have highlighted the recent development in understanding the relationship of the human microbiome with cancer and also emphasize on various roles of the microbiome in the modulation of cancer therapy. Additionally, we also summarize the ongoing research focussed on the improved efficacy of chemotherapy and immunotherapy using the host microbiome.

Excited-State Intramolecular Hydrogen-Bonding-Assisted Restricted Rotation: A Mechanism for Monitoring Intracellular Viscosity and Distinguishing Malignant, Differentiating, and Apoptotic Cancer Cells.

We have successfully developed a sensor (IP1) that utilizes a confocal-based live-cell imaging technique for distinguishing malignant, differentiating, and under-apoptosis cancer cells. The intracellular viscosity (IVis) is minimum in the cancer cell, intermediate in differentiating cells, and maximum in the apoptotic cells. Therefore, we have developed a molecular rotor (IP1) that can sense the changes in intracellular viscosity. IP1 works on the viscosity-assisted restricted-rotation mechanism and is facilitated by the excited-state intramolecular hydrogen-bonding phenomenon (ESIHB). The use of ESIHB has fine-tuned the viscosity-sensing properties of IP1, which in turn has greatly helped in our quest of distinguishing the malignant, differentiating, and apoptotic cancer cells by the IP1 probe. It was very effective in monitoring apoptosis by increased fluorescence intensity by the confocal live-cell imaging technique. The noncytotoxic behavior, even at 10 µg/mL concentration, is a charming feature of the developed probe. To the best of our knowledge, this is the first report for the ESIHB-based fluorescence probe that can distinguish malignant, differentiating, and apoptotic cancer cells by the use of live-cell imaging techniques.