Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence

Understanding protein sequence and structure is essential for understanding protein-protein interactions (PPIs), which are essential for many biological processes and diseases. Targeting protein binding hot spots, which regulate signaling and growth, with rational drug design is promising. Rational drug design uses structural data and computational tools to study protein binding sites and protein interfaces to design inhibitors that can change these interactions, thereby potentially leading to therapeutic approaches. Artificial intelligence (AI), such as machine learning (ML) and deep learning (DL), has advanced drug discovery and design by providing computational resources and methods. Quantum chemistry is essential for drug reactivity, toxicology, drug screening, and quantitative structure-activity relationship (QSAR) properties. This review discusses the methodologies and challenges of identifying and characterizing hot spots and binding sites. It also explores the strategies and applications of artificial-intelligence-based rational drug design technologies that target proteins and protein-protein interaction (PPI) binding hot spots. It provides valuable insights for drug design with therapeutic implications. We have also demonstrated the pathological conditions of heat shock protein 27 (HSP27) and matrix metallopoproteinases (MMP2 and MMP9) and designed inhibitors of these proteins using the drug discovery paradigm in a case study on the discovery of drug molecules for cancer treatment. Additionally, the implications of benzothiazole derivatives for anticancer drug design and discovery are deliberated.

Elevated HSP70 and HSP90 as Predictive Markers of Immune Activation and Lung Injury in SARS-COV-2 Disease

Background

Heat shock proteins (HSPs) are involved in innate and adaptive immune responses, especially inflammatory responses due to immune cell activation. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was one of the most important causes of death in the recent pandemic. Increased cellular stress and excessive inflammation are common in coronavirus disease-19 (COVID-19), although the underlying mechanisms are still poorly understood.

Objective

To evaluate the relationship between HSP and the pathological effects of COVID-19.

Methods

A group of 107 patients was categorized to two populations (mild and severe) based on their chest high-resolution computed tomography (HRCT) results. The HSP70, HSP90 alpha, and serum levels of C-reactive protein (CRP) were measured by enzyme-linked immunosorbent assay (ELISA). Lactate dehydrogenase (LDH), and creatine phosphokinase (CPK) were measured by the automated analyzer.

Results

Our data showed increased levels of HSP70 and HSP90 in patients with COVID-19. The HSPs levels were elevated in the severe group compared to the mild group. This study demonstrated a positive correlation between both elevated levels of HSP70, HSP90, and HRCT grade and also a positive correlation with CRP and CPK in the severe group.

Conclusion

HSP90 and HSP70 contribute to excessive immune responses and cytokine storms. They may serve as prognostic serum markers for COVID-19 lung injury. Additionally, they are candidates for anti-inflammatory therapy.

Salivary protein biomarkers for diagnosis of oral squamous cell carcinoma

OSCC (Oral Squamous Cell Carcinoma) is a major health challenge in many parts of the world. It occurs most commonly in males and is associated with tobacco, pan, or areca nut consumption. One of the major challenges associated with the management of OSCC is late diagnosis. As a result, the treatment required is more aggressive, expensive, and has poor prognostic value. On the other hand, early diagnosis of OSCC can be life-saving with less aggressive treatment and a better prognosis. A diagnostic method for early diagnosis of OSCC is greatly needed. A lot of research efforts have been made to identify biomarkers that can act as tools to classify the tumor status of the patient. Various biological fluids and tissues have been explored for such studies. Saliva appears to be the most attractive biological sample with many potential advantages over other matrices such as blood or tissue. Saliva as a diagnostic fluid has the advantage of ample availability, being non-invasive and being in the vicinity of the tumor, and having a less complex composition. Our paper provides an updated review of the state of the art of research in the area of salivary biomarkers for oral squamous cell carcinoma. The paper gives an account of methods for saliva collection, followed by a brief description of various protein biomarkers discovered to date, along with their status quo.

The Heat Shock Connection: Skeletal Muscle Hypertrophy and Atrophy

Skeletal muscle is an integral tissue system that plays a crucial role in the physical function of all vertebrates and is a key target for maintaining or improving health and performance across the lifespan. Based largely on cellular and animal models, there is some evidence that various forms of heat stress with or without resistance exercise may enhance skeletal muscle growth or reduce its loss. It is not clear whether these stimuli are similarly effective in humans or meaningful in comparison to exercise alone across various heating methodologies. Furthermore, the magnitude by which heat stress may influence whole body thermoregulatory responses and the connection to skeletal muscle adaptation remains ambiguous. Finally, the underlying mechanisms, which may include interaction between relevant heat shock proteins and intracellular hypertrophy and atrophy related factors, remain unclear. In this narrative mini-review we examine the relevant literature regarding heat stress alone or in combination with resistance exercise emphasizing skeletal muscle hypertrophy and atrophy across cellular and animal models, as well as human investigations. Additionally, we present working mechanistic theories for heat shock protein mediated signaling effects regarding hypertrophy and atrophy related signaling processes. Importantly, continued research is necessary to determine the practical effects and mechanisms of heat stress with and without resistance exercise on skeletal muscle function via growth and maintenance.

Ex vivo Optimization of Glucose-Regulated Protein 94/Glycoprotein 96 Expressions in Mammospheres; Implication for Breast Cancer Immunotherapy

OBJECTIVE

The induction of immunity against cancer stem cells (CSCs) can boost the efficiency of cancer vaccines. Heat shock proteins (HSPs) are required for the successful activation of anti-tumor immune responses. Glycoprotein 96 (gp96) is a well-known HSP that promotes the cross-presentation of tumor antigens. The aim of the present study was to optimize the temperature for induction of gp96 in grade 3 breast cancer spheres.

MATERIALS AND METHODS

In the experimental study, CSCs were enriched from breast tumor tissue samples and cultured in DMEM-F12 with epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), B27, and bovine serum albumin (BSA) for 22 days. The expression level of CD24 and CD44 as CSC markers was measured by flow cytometry in secondary mammospheres, and the expression of NANOG, SOX2, and OCT4 genes in CSCs was also analyzed using the real-time polymerase chain reaction (PCR). To find the optimal temperature regulation of gp96, the mammosphere was incubated at different temperatures for 1 hour, and gp96 expression was measured using the western blotting assay.

RESULTS

Primary mammospheres were obtained after seven days of culture, and secondary spheres formed 22 days after passage. Flow cytometry analysis showed that cells with CD24^- CD44⁺ phenotype were enriched in the culture period (from 2.6% on day 1 to 32.6% on day 22). Real-time PCR indicated that OCT4, NANOG, and SOX2 expression in mammospheres were increased by 3.8 ± 0.6, 17.8 ± 0.6, and 7.7 ± 0.8 fold respectively in comparison to the MCF-7 cell line. Western blot analysis showed that gp96 production was significantly upregulated when mammospheres were incubated at both 42°C and 43°C in comparison to the control group.

CONCLUSION

Altogether, we found that heat-induced upregulated expression of gp96 in CSCs enriched mammospheres from breast tumor tissue might be used as a complementary procedure to generate more immunogenic antigens in immunotherapy settings.

Moderate-Intensity Exercise Training in Association with Insulin Promotes Heat Shock Proteins 70 and 90 Expressions in Testicular Tissue of Experimental Type 1 Diabetes

Objective

The current research was designed to analyze the effect of moderate-intensity exercise training (MEXT), solely and simultaneous with insulin, on the network between oxidative stress and Hsp70 and Hsp90 chaperones after experimental type I diabetes (DM) induction in rats.

Materials and Methods

In the experimental study, 36 mature Wistar rats were assigned into control and experimental type I DM-induced groups, and then the diabetic animals were categorized to sedentary type I DM-induced (SDM), exercise training-sole without DM (E), exercise training DM-induced (EDM), insulin-treated sedentary DM-induced (ISDM), and exercise training insulin-treated DM-induced (EIDM) groups. After 6 weeks, Johnson’s score was evaluated to analyze the spermatogenesis ratio.

Results

The Hsp70 and Hsp90 expression levels, testicular total antioxidant capacity (TAC), protein peroxidation ratio, testicular DNA fragmentation ratio, and mRNA damage were investigated. The animals in EDM and EIDM groups (solely and simultaneously) represented a significant (P<0.05) improvement in Johnson’s score, spermatogenesis, and TAC ratios versus SDM animals. Moreover, the DM-induced DNA and mRNA damage and protein peroxidation ratio were significantly (P<0.05) recovered in EDM and ISDM groups, which was more remarkable in the EIDM group. The EDM and EIDM groups exhibited significant (P<0.05) increment in Hsp70 and Hsp90 expression levels versus the control and SEDT1 animals. However, the EIDM group exhibited no significant changes compared to the control animals.

Conclusion

The EX could ameliorate the EDT1-induced detrimental impact by up-regulating Hsp70 and Hsp90 expressions. Meanwhile, it exerts potentially more effective impact, when it is considered simultaneously with insulin therapy.

Differential Modulation of Heat-Inducible Genes Across Diverse Genotypes and Molecular Cloning of a sHSP From Pearl Millet [Pennisetum glaucum (L.) R. Br.]

The survival, biomass, and grain yield of most of the crops are negatively influenced by several environmental stresses. The present study was carried out by using transcript expression profiling for functionally clarifying the role of genes belonging to a small heat shock protein (sHSP) family in pearl millet under high-temperature stress. Transcript expression profiling of two high-temperature-responsive marker genes, Pgcp70 and PgHSF, along with physio-biochemical traits was considered to screen out the best contrasting genotypes among the eight different pearl millet inbred lines in the seedling stage. Transcript expression pattern suggested the existence of differential response among different genotypes upon heat stress in the form of accumulation of heat shock-responsive gene transcripts. Genotypes, such as WGI 126, TT-1, TT-6, and MS 841B, responded positively toward high-temperature stress for the transcript accumulation of both Pgcp70 and PgHSF and also indicated a better growth under heat stress. PPMI-69 showed the least responsiveness to transcript induction; moreover, it supports the membrane stability index (MSI) data for scoring thermotolerance, thereby suggesting the efficacy of transcript expression profiling as a molecular-based screening technique for the identification of thermotolerant genes and genotypes at particular crop growth stages. The contrasting genotypes, such as PPMI-69 (thermosusceptible) and WGI-126 and TT-1 (thermotolerant), are further utilized for the characterization of thermotolerance behavior of sHSP by cloning a PgHSP16.97 from the thermotolerant cv. WGI-126. In addition, the investigation was extended for the identification and characterization of 28 different HSP20 genes through a genome-wide search in the pearl millet genome and an understanding of their expression pattern using the RNA-sequencing (RNA-Seq) data set. The outcome of the present study indicated that transcript profiling can be a very useful technique for high-throughput screening of heat-tolerant genotypes in the seedling stage. Also, the identified PgHSP20s genes can provide further insights into the molecular regulation of pearl millet stress tolerance, thereby bridging them together to fight against the unpredicted nature of abiotic stress.

Chronic heat treatment positively impacts metabolic profile of ovariectomized rats: association with heat shock response pathways

Low estrogen levels may predispose women to increased bodyweight and dyslipidemia. Previous studies from our laboratory suggest an involvement of depressed heat shock response (HSR) in this scenario because estrogen potently stimulates HSR. As heat treatment induces the expression of the anti-inflammatory heat shock proteins of the 70-kDa family (HSP70) and its accompanying HSR, we aimed to investigate whether chronic heat treatment promotes beneficial effects on biometric, lipid profile, oxidative stress, and HSR in ovariectomized rats. Wistar adult female rats (n = 32) were divided into four groups: control (C, n = 7), ovariectomized (OVX, n = 9), heat-treated (HT, n = 9), and heat-treated ovariectomized rats (OVX+HT, n = 7). HT and OVX+HT rats were anesthetized and submitted to heat treatment (once a week for 12 weeks) in a water bath (41 °C) to increase rats' rectal temperature up to 41 °C for 15 min, while C and OVX animals were submitted to a 36 °C water bath. HT attenuated the weight gain induced by OVX and increased HDL cholesterol and triglyceride serum levels. Also, OVX rats showed increased total cholesterol and LDL cholesterol levels that were not influenced by HT. Interestingly, it was found that an overall trend for HT to decrease tissue catalase and superoxide dismutase antioxidant activities was paralleled by a decrease in malondialdehyde levels (indicative of lower lipoperoxidation), especially in the skeletal muscle. Surprisingly, OVX was not able to depress intracellular HSP70 expression in the skeletal muscle, as expected, and this remained unchanged with HT. However, chronic HT did enhance intracellular HSP70 contents in white adipose tissue of OVX animals. As both glucose and insulin tolerance tests were not affected by OVX, which was not modified by HT, we suppose that estrogen absence alone is not sufficient to determine a state of insulin resistance associated with low intramuscular HSP70 content.

Exogenous Ascorbic Acid Induced Chilling Tolerance in Tomato Plants Through Modulating Metabolism, Osmolytes, Antioxidants, and Transcriptional Regulation of Catalase and Heat Shock Proteins

Chilling, a sort of cold stress, is a typical abiotic ecological stress that impacts the development as well as the growth of crops. The present study was carried to investigate the role of ascorbic acid root priming in enhancing tolerance of tomato seedlings against acute chilling stress. The treatments included untreated control, ascorbic acid-treated plants (AsA; 0.5 mM), acute chilling-stressed plants (4 °C), and chilling stressed seedlings treated by ascorbic acid. Exposure to acute chilling stress reduced growth in terms of length, fresh and dry biomass, pigment synthesis, and photosynthesis. AsA was effective in mitigating the injurious effects of chilling stress to significant levels when supplied at 0.5 mM concentrations. AsA priming reduced the chilling mediated oxidative damage by lowering the electrolyte leakage, lipid peroxidation, and hydrogen peroxide. Moreover, up regulating the activity of enzymatic components of the antioxidant system. Further, 0.5 mM AsA proved beneficial in enhancing ions uptake in normal and chilling stressed seedlings. At the gene expression level, AsA significantly lowered the expression level of CAT and heat shock protein genes. Therefore, we theorize that the implementation of exogenous AsA treatment reduced the negative effects of severe chilling stress on tomato.

Evaluation of immuno-modulating effect of recombinant heat shock protein 40 of Brucella abortus in mice

The present study was aimed to evaluate the immuno-modulatory effect of Brucella-specific recombinant HSP40 (rDnaJ) when co-immunized with Brucella rOmp22 in mice. For this, dnaJ of Brucella abortus was cloned, expressed in E. coli, and purified to homogeneity using Ni-NTA agarose columns. Three groups of mice (n = 6 in each group) were used in the study. The control group was immunized with rOmp22 alone, while group 1 mice were injected subcutaneously with rOmp22 along with conventional adjuvants (FCA, FIA), and group 2 mice with rOmp22 mixed with rDnaJ. IgG isotype (IgG1 and IgG2a) response to rOmp22 immunization was evaluated by enzyme-linked immunosorbent assay which was found to be directed towards the cell-mediated arm of immune system (CMI) in group 2 mice in which rOmp22 was co-immunized with rDnaJ. Expression profiling of IL-4 and IL-12 was checked in all the groups by qRT PCR. IL12 mRNA was up-regulated to a greater extent in group2 mice, suggesting that the CMI arm of immune system was stimulated. Hence, it was concluded that CMI response against rOmp22 is stimulated to a greater extent in mice when co-immunized with Brucella rDnaJ.

The Unmysterious Roles of HSP90: Ovarian Pathology and Autoantibodies

The heat shock proteins (HSPs) are a group of evolutionarily conserved proteins with important physiological functions, whose synthesis is enhanced by elevated temperature or other stresses. HSPs show high sequence homology between different species, from bacteria to humans. Despite the significant degree of evolutionary conservation, HSPs are highly immunogenic. Of the several HSPs, HSP90 is an abundant, constitutively expressed chaperone constituting around 1-2% of total cellular protein under non-stress conditions. This protein from even the most distantly related eukaryotes has 50% amino acid identity, and all have more than 40% identity with the Escherichia coli protein. They are immunodominant antigens for many common microbes, and thus their epitopes are recognized by the immune system. As HSPs are overexpressed at sites of acute and chronic inflammation, individuals are likely to be sensitized during the course of a microbial infection encountered during life. This chapter considers the evidence of a role for HSP90 in autoimmune ovarian failure, where autoantibodies to it have been observed in patients, and has been correlated to infertility.

Functional evaluation of Heat Shock Proteins 70 (HSP70/HSC70) on Rhodnius prolixus (Hemiptera, Reduviidae) physiological responses associated with feeding and starvation

Blood-sucking vectors must overcome thermal stress caused by intake of proportionally large amounts of warm blood from their hosts. In response to this, Heat Shock Proteins (HSPs) such as the widely studied HSP70 family (the inducible HSP70 and the cognate form HSC70, known for their role in preserving essential cellular functions) are rapidly up-regulated in their tissues. The triatomine Rhodnius prolixus is an important vector of Trypanosoma cruzi, the causative pathogen of Chagas' disease, and is also a model organism for studying insect biology and physiology. In this work, we observed that the expression of Rhodnius prolixus HSP70 was rapidly up-regulated in response to thermal shocks (0 °C and 40 °C) and also during the first hours after feeding on blood. HSP70/HSC70 RNAi knockdown elicited important alterations in R. prolixus physiological responses triggered by blood meal and starvation. HSP70/HSC70 knockdown insects showed lower resistance to prolonged starvation in comparison to appropriate controls, dying between 32 and 40 days after dsRNA injection. After blood feeding, the physiological effects of HSP70/HSC70 knockdown were more prominent and the insects died even earlier, within 14-20 days after feeding (21-27 days after dsRNA injection). These bugs showed impaired blood processing and digestion, reduced energetic metabolism and the midgut immune responses were compromised. Our findings suggest that HSP70/HSC70 depletion affected R. prolixus in starvation or fed conditions. After feeding, the arrival of blood in the digestive tract of knockdown insects fails to activate essential signaling pathways involved in blood processing, producing several alterations in their physiological processes enough to generate a premature death.

Identification of Heat Shock Protein families and J-protein types by incorporating Dipeptide Composition into Chou's general PseAAC

Heat Shock Proteins (HSPs) are the substantial ingredients for cell growth and viability, which are found in all living organisms. HSPs manage the process of folding and unfolding of proteins, the quality of newly synthesized proteins and protecting cellular homeostatic processes from environmental stress. On the basis of functionality, HSPs are categorized into six major families namely: (i) HSP20 or sHSP (ii) HSP40 or J-proteins types (iii) HSP60 or GroEL/ES (iv) HSP70 (v) HSP90 and (vi) HSP100. Identification of HSPs family and sub-family through conventional approaches is expensive and laborious. It is therefore, highly desired to establish an automatic, robust and accurate computational method for prediction of HSPs quickly and reliably. Regard, a computational model is developed for the prediction of HSPs family. In this model, protein sequences are formulated using three discrete methods namely: Split Amino Acid Composition, Pseudo Amino Acid Composition, and Dipeptide Composition. Several learning algorithms are utilized to choice the best one for high throughput computational model. Leave one out test is applied to assess the performance of the proposed model. The empirical results showed that support vector machine achieved quite promising results using Dipeptide Composition feature space. The predicted outcomes of proposed model are 90.7% accuracy for HSPs dataset and 97.04% accuracy for J-protein types, which are higher than existing methods in the literature so far.

A comparative study on biologically and chemically synthesized silver nanoparticles induced Heat Shock Proteins on fresh water fish Oreochromis niloticus

The wide applicability of silver nanoparticles in medicine and pharmaceutical industries leads to its over exploitation and thus contaminating our environment. Majority of these nanoscale dimension particles finally accumulates in fresh water and marine ecosystem. As the nanoparticles behave entirely different from its corresponding bulk material, a better understanding of their environmental impacts in aquatic ecosystems is inevitable. The study was focused on a comparative stress physiology analysis of chemically synthesized silver nanoparticles and biogenic silver nanoparticles. Half maximal inhibitory concentration of biologically synthesized and chemically synthesized nanoparticles was found out (30μg/mL and 20μg/mL respectively). The Heat Shock Protein (HSP70) secretion was analysed in the fresh water fish Oreochromis niloticus after exposing to different concentrations of biologically and chemically synthesized silver nanoparticles along with the silver in its ionic form. The intense immune-histochemical staining of fish tissues (muscle, kidney and liver) analyzed proportionately reflected the stress created. The colour intensity was directly proportional to the stress created or the stress protein released. High level of HSP70 expression was observed in all of the fish tissues exposed to silver ions and chemically synthesized silver nanoparticles, when compared to that of biologically synthesized. The results revealed the significance of comparatively safe and less toxic biogenic nanoparticles compared to the chemically synthesized.