The obligate intracellular parasitic protozoa of genus Leishmania are an etiological agent of a complex vector-borne zoonotic disease named leishmaniasis. It gets transmitted by more than 20 species of sand fly vectors of the genera Phlebotomus and Lutzomyia (Djune Yemeli et al., 2021). According to the 2010 WHO expert committee report, different clinical manifestations that occurred in the Old World are classified into three primary forms: 1) visceral leishmaniasis (VL), also known as kala-azar, caused by L. donovani and L. infantum; 2) cutaneous leishmaniasis (CL), most frequently caused by L. tropica, L. major, and L. aethiopica; and 3) mucocutaneous leishmaniasis (MCL) (can be caused by any species). 4) diffused cutaneous leishmaniasis (caused by L. aethiopica) and 5) post kala-azar dermal leishmaniasis (present in all areas with L. donovani). While CL is the most common form of the disease, VL is the most serious and is almost always fatal if untreated (Colmenares et al., 2002).

Autophagy is a climacteric cellular catabolic process to maintain cellular homeostasis, and it is conserved in a hierarchy from yeasts to mammals. The term autophagy was coined by Christian de Duve in 1963, but it remained a biological enigma until the early 1990s (De_Duve, 1974- Lysotropic. pdf). Furthermore, in the early 1990s, Yoshinori Ohsumi, an Assistant Professor at Tokyo University, studied autophagy using the budding yeast Saccharomyces cerevisiae as a model system and revealed some basic phenomena of the autophagy. He also discovered gene autophagy 1 (APG1), which is responsible for autophagy in yeast, and reported 15 more APG genes responsible for autophagy in the eukaryotic cell yeast. Autophagic genes were further identified in yeast and other species, and this specific group of proteins is abbreviated as ATG (Tsukada and Ohsumi, 1993), (Matsuura et al., 1997). All cells engage in low-level basal autophagy to carry out homeostatic functions like protein and organelle turnover. When cells produce intracellular nutrients and energy, such as during deprivation, growth factor depletion, or high bioenergetic demands, it is quickly activated. Furthermore, autophagy is activated when cells are ready to undergo structural remodeling, such as during developmental transitions, or when they need to get rid of potentially harmful cytoplasmic elements, such as under oxidative stress, infection, or the buildup of protein aggregates. Regulation of autophagy is significantly influenced by nutritional status, hormonal factors, and other factors like temperature, oxygen concentrations, and cell density (Klionsky, 2007), (Maiuri et al., 2007).

To date, collectively 41 types of proteins are known to play an important role in autophagy in different groups on the basis of their functions. These proteins are classified into six functional groups: ATG1-kinase/ULK1 complex, phosphatidylinositol (PI) 3-kinase complex (PI3K), membrane protein ATG9, ATG2–ATG18 complex, ATG16L conjugation system, and ATG8 conjugation system (Mizushima et al., 2011). These proteins and their homologs are well-studied in yeast as well as in mammals (C. He & Klionsky, 2009).

Initiation of autophagosome formation in mammals is a complicated process, orchestrated by three major proteins ULK1 (unc-51-like kinase 1) ATG13, FIP200 (focal adhesion kinase family interacting protein of 200 kDa), and ATG101 combined to form the ULK1 complex. Succeeding autophagy induction, the ULK1 complex translocates to the autophagophore membrane or autophagy initiation site and further regulates PI3K complex recruitment over the autophagophore. This PI3K complex includes the VPS (vacuolar protein sorting) 34 (VPS34) complex, class III phosphatidylinositol 3-kinase VPS34, Beclin-1, VPS15, and ATG14L (ATG14-like), which govern the production of the phospholipid phosphatidylinositol 3-phosphate (PI3P) at the autophagophore. WIPI (WD repeat domain phosphoinositide interacting protein 2) and DFCP1 (double FYVE-containing protein 1) are recruited at the PI3P binding site and contribute to autophagophore expansion (Zachari & Ganley, 2017), (Bento et al., 2016). PI3P acts as a crucial component where numerous proteins are recruited and helps in autophagosome formation. ATG2 interacts with ATG18, which acts as a PI3P-binding partner, and forms a complex that further translocates to autophagophores and contributes to autophagosome biogenesis (Kotani et al., 2018).

In participation with the PI3K complex, ATG9 is playing a crucial role in lipid accumulation on the autophagophore and its expansion; ATG9 is a multi-spanning membrane protein (Geng et al., 2008), (Webber & Tooze, 2010), (Kotani et al., 2018). The exact molecular role of ATG2, as well as ATG9, is still mysterious, but directly or indirectly, they contribute to the PI3K complex for autophagosome initiation and expansion. Along with these complexes, two major autophagy-specific ubiquitin-like protein conjugation systems play a crucial role in autophagosome formation and maturation. It begins with the ATG16L conjugation system that consists of the ATG12–ATG5 conjugate covalently linked by ubiquitin-like enzymes ATG7 and ATG10 that act as E1 and E2-like enzymes, respectively. In addition, for localization of this conjugate on the autophagosome membrane, ATG16L is required. The ATG12–ATG5 conjugate and ATG16L that interact non-covalently are recruited on the membrane, whereas ATG5 mediates the interaction leading to autophagosome expansion (Romanov et al., 2012), (Noda et al., 2013). The ATG12–ATG5 conjugate has been shown to mediate LC3II–PE complex formation, while the ATG16L complex is observed to stabilize this complex on the membrane. In addition to acting as a marker for autophagy, the LC3II–PE conjugate is an essential step in the production of autophagosomes. Formation of the LC3II–PE conjugate is mediated by ATG4, which acts as a cysteine protease and cleaves ATG8 from the C-terminus at arginine and exposes the glycine residue and allows it to interact with PE (phosphatidyl ethanolamine) (Maruyama and Noda, 2018). This glycine-exposed LC3 and PE interaction is facilitated by ATG7, an E1-like enzyme that transfers LC3I to an E3-like enzyme and subsequently transfers LC3I to the membrane lipid PE, and LC3II complex translocates on the autophagosome. Autophagosome maturation takes place by various ATG protein complexes, as shown in Figure 3.

Autophagy processes are involved in strategies to eliminate invasive pathogens through the production of reactive oxygen species, adjustment of vital nutrients and cations, destruction by proteolytic enzymes (Galán and Cossart, 2005), and by playing a crucial role in host–pathogen interaction, especially in intracellular pathogenesis. Research conducted over the last few years suggests that autophagy is one of the most astonishing intracellular host cell defense machinery tools that pathogens must spread during cell invasion. During infection, autophagosomes engulf intracellular pathogens; this process is known as xenophagy since it results in the eradication of foreign material. Pathogens are engulfed during autophagy and bind to the autophagosome membrane protein LC3 (light-chain 3)/Atg8 (autography-related protein 8).

To establish a persistent infection, most intracellular pathogens manipulate the autophagy pathway at the molecular level (Campoy and Colombo, 2009). Toll-like receptors (TLRs) that identify pathogen-associated molecular patterns induce autophagy during infection and allow autophagy to kill the pathogen. TLR signaling cascade and autophagy are two innate defense mechanisms that allow intracellular parasite clearance (Delgado et al., 2008). TLRs recognize conserved microbial components and induce a variety of antimicrobial activities, such as xenophagy via Myd88 and TRIF interacting with Beclin 1 (Campos-Salinas et al., 2013), (Shi and Kehrl, 2008). Autophagy also gets induced by cell-to-cell signaling. In human cells, IFN-γ stimulates autophagy through IRGM1, whereas CD40 ligation causes autophagy through PI3K and Rab7, enabling cells to fight intracellular infections like Toxoplasma gondii (Andrade et al., 2006).

Several molecules, including Nod-1 and Nod-2, recognize microbial antigen peptidoglycans and target bacteria for xenophagy (Cooney et al., 2010), (Travassos et al., 2010). However, many pathogens escape the phagosome after phagocytosis and proliferate in the cytosol. Microbes can also promote xenophagy via a variety of cell stress mechanisms, whereas T. gondii increases intracellular calcium levels to promote autophagy (Singh et al., 2009). Studies of Group A streptococci (GAS) also show evidence of autophagy. Getting rid of GAS (escapes from endosomes by encoding the hemolytic toxin streptolysin O) is a great illustration of autophagy, where ATG5 associates with ATG8/LC3 to form autophagic vacuoles for clearance of GAS (Nakagawa et al., 2004).

In the extensively studied pathogen Mycobacterium tuberculosis (Mtb), the removal of bacteria by autophagy, IFN (interferon)-induced IRGs (immunity-related p47 GTPases), and the overexpression of LRG-47 (one of the 23 IRGs in mice) promote autophagosome formation and autophagy-dependent clearance of phagosomes containing Mtb in mice (Gutierrez et al., 2004). Both mouse IRGs and autophagy can target the phagosomes that T. gondii uses for replication during toxoplasmosis. In contrast to the macroautophagy upregulating effect found for IRGs during Mtb infection, the mouse IRGs, IIGP1 and IGTP, appear to disrupt the T. gondii-contained PV (parasitophorous vacuole) membrane and even the parasite’s membrane, exposing it for destruction via macroautophagy (Tang et al., 2006), (Romanov et al., 2012). An effective illustration of evading autophagosome engulfment is T. cruzi (the causative agent of Chagas disease) infection to mammalian cells and activation of a signal transduction cascade that results in the establishment of a parasitophorous vacuole. Lysosomes have a significant impact on how T. cruzi infections progress, according to studies. The T. cruzi vacuole is decked with the host cell autophagic protein LC3. Fasting or pharmacologically induced autophagy increased the number of infected cells dramatically before infection, while inhibitors of this process significantly decreased the invasion, showing that mammalian autophagy is an important process that favors colonization of T. cruzi in the host cell (Alvarez et al., 2008). Skin lesions from BALB/c mice having CL also exhibit autophagy. In cultured macrophages, autophagy inhibitor 3-methyladenine (3 MA) decreased the infection index, while autophagy-inducing agents like rapamycin or fasting had no effects. This finding suggests that one function of autophagy is to provide nutritional support during infection (Cyrino et al., 2012).

In a comparative study of L. major and L. amazonensis, both species of infected macrophages demonstrated an increase in the LC3-II/Act (autophagic marker) ratio after 24 h, although treatment with autophagic inhibitors had no discernible effect on the parasite burden or infection rate. It is noteworthy to observe that pharmacological autophagy inducers increase parasite survival, whereas pharmacological autophagy inhibitors have no effect on it (Dias et al., 2018).

Researchers have become more interested in autophagy in leishmaniasis despite contradictory findings concerning the importance of autophagy in leishmaniasis. The reason is autophagy has been evidenced to be a therapeutic target in several intracellular pathogeneses, inflammatory illnesses, metabolic disorders, diabetes, cancer, osteoporosis, and other conditions.

Literature on leishmaniasis focuses on the interaction between lipid metabolism and autophagy. Both autophagy and lipid metabolism are necessary for creation of new perspectives on the investigation of leishmanial therapy. We are aware of very few articles that discuss the significance of lipid metabolism and autophagy. In this review, we try to highlight these crucial processes concerning therapeutics.

The effect of autophagy on parasite survival and its modulation made by the parasite for its own survival establishing the host autophagy pathway serves as a possible therapeutic target in the treatment of leishmaniasis. Available information highlighted a few of the protein molecules which can serve as a target for future therapeutic purposes against leishmaniasis.

Leishmania-infected human monocyte-derived macrophages (hMDMs) lead to stimulation of autophagy LC3-associated phagocytosis (LAP), which has an even sharper effect on decreasing proliferation by inhibiting CD4⁺ T-cell growth and proliferation of CD4⁺ T-cells, leading to a reduced intracellular parasite survival. This further implies that host cell autophagy modulates the T-cell response, enhances parasite persistence, and yet has no effect on the viability of the parasite. Apparently, Leishmania utilizes the autophagy mechanism of the host cells to inhibit T-cell proliferation and highlights the autophagy mechanism (Crauwels et al., 2015). CD4⁺ Th1 cell-mediated immunity is required for protective immunity against leishmaniasis (Okwor et al., 2014), (Peters et al., 2014) because the progression of the parasite is due to the exhaustion of T cells; however, the mechanism involved is not clearly understood (Esch et al., 2013).

Blocking PDL-1 signaling in vivo leads to reinstatement of protective type 1 response by both CD4⁺ and CD8⁺ T cells, and as a result, the parasite burden was significantly reduced. Inhibition of PDL-1 enhanced the production of TNF, IL-12, reactive oxygen species (ROS), and nitric oxide (NO) and significantly reduced parasite survival (Roy et al., 2019). Mechanistically, PDL-1 inhibition blocked the autophagy process (Robainas et al., 2017) hijacked by Leishmania to acquire host cell nutrients for their survival (Crauwels et al., 2015). The restoration of effector arms of protective immunity against leishmaniasis and subsequent parasite clearance can be achieved with anti-PDL-1 antibody therapy (Robainas et al., 2017).

The anti-pathogen properties of mammalian target of rapamycin (mTOR) have been proven, as well as its ability to prevent autophagy (Rangwala et al., 2014). Leishmania promotes the PI3K pathway in the host, and PI3K activation inhibits autophagy via enhancing mTOR (Ruhland et al., 2007). The ability of different mTOR inhibitors such as rapamycin, GSK-2126458, and KU-0063794 was evaluated by administering to infected BALB/c mice. In contrast to KU-0063794, rapamycin or GSK-2126458 significantly reduced the parasite load (Khadir et al., 2018) in the draining lymph node as well as the swelling of the footpad. Other studies demonstrated that pre-treatment of host cells with rapamycin to induce autophagy prior to infection was inhibitory to survival of parasites in a concentration-dependent manner, and once infection is established, the stimulation of autophagy by Leishmania confers the advantage of parasite survival.

Thomas et al. (2018) suggested that Leishmania infection delayed induction of host cell autophagy that is essential for the best possible intracellular survival. L. donovani boosted AKT activation to control the GSK-3/-catenin/FOXO-1 axis, preventing host cell apoptosis and immune response necessary for the survival of the parasite in macrophages (Gupta et al., 2016). Taken together, mTOR inhibitors or the PI3K/Akt pathway are used in therapeutic settings for managing leishmaniasis (Madeira Da Silva and Beverley, 2010), (Khadir et al., 2018), (Thomas et al., 2018).

Leishmania infection significantly induces the expression of SIRT1, which inactivated FOXO-1 through deacetylation, constitutively active FOXO-1 led to increased cell death, thereby suggesting that nuclear FOXO-1 might be inactivated (Gutierrez et al., 2004). SIRT1 knockdown led to increased apoptosis and significantly decreased parasite survival along with increased production of TNF-α, ROS, and NO. SIRT1 inhibitor sirtinol in infected mice shows a synergistic effect found with the PD-1 inhibitor. Although they are interconnected, the SIRT1/FOXO-1 axis is used by Leishmania to differentially regulate PD-1 signaling, and both pathways alone support intracellular parasite persistence (Roy et al., 2019).

The parasite uses the PERK/ATF4 pathway, which is crucial for maintaining protein homeostasis and establishing infection (Abhishek et al., 2018). Additionally, PERK signaling reduces translation and promotes ATF4 expression, which either promotes cell survival or causes cell death. Cytoprotective autophagy genes, ATG5 and ATG7, are known to be upregulated as a result of PERK/ATF4 pathway activation (Zheng et al., 2019), which favors cellular survival and parasite infection (Aoki et al., 2019). GSK2606414 previously used as an anti-cancerous drug was discovered through chemical inhibition tests to assess prospective drugs since it targets the kinase domain of PERK (Rangwala et al., 2014), and its therapeutic implications and role in leishmanial infection may substantiate it as a repurposed drug for treatment options for leishmaniasis.

PGE₂ (prostaglandin E2) is responsible for the increment in parasite load in macrophages (Ribeiro-Gomes et al., 2004), and the physiological stimulation of autophagy promotes the intracellular survival of L. amazonensis by a process involving increases in the synthesis of lipid bodies and PGE2, as well as lower NO levels (Vallochi et al., 2018). Also, Martínez and Ruiz (2019) stated that lysosomes destroy LDs after autophagosomes sequester it during lipophagy. Growing evidence points to the involvement of LDs in the control of the autophagic process and their eradication by autophagy via lipophagy. Thus, blocking autophagy-mediated process via lipid droplets may serve as a newer area to combat leishmaniasis.

Recent research has shown that the host microRNA, MIR30A-3p, may regulate host autophagy following L. donovani infection. After L. donovani infection, MIR30A-3p expression is significantly increased in a time-dependent manner. MIR30A-3p mimic decreased and with antagomir increased the expression of BECN1 protein in L. donovani-infected macrophages, demonstrating the role of MIR30A-3p in autophagy in leishmaniasis (Singh et al., 2016). Autophagy and miRNAs are interconnected (Frank et al., 2015). BMDM showed intracellular amastigote clearance by autophagy in BMDM through mTOR phosphorylation-dependent counteracting mechanism after in vitro infection with L. major. Additionally, the study demonstrates a relationship between the infection-specific overexpression of (BCL2/adenovirus E1B 19 kDa protein-interacting protein) BNIP3 and (cathepsin-E) CTSE and autophagy-related protein 5 (ATG5). There is evidence for showing the involvement of miR-101c, miR-129, and miR-210 in RNA-level autophagy regulation during L. major infection and miRNAs have been linked to lipid metabolism, not in leishmaniasis but in other disorders (Latorre et al., 2017).

Altogether in L. major-infected host macrophages, autophagy is a tightly controlled cellular process at the RNA and protein levels (Frank et al., 2015), suggesting a role of RNAs in the modulation of autophagy in leishmaniasis.

A new era is emerging where people are trying to combat fatal situations with the use of microRNAs. So, in this review, we elaborate on the collaborative functioning of microRNAs with lipid-mediated autophagy, and the respective probability of incorporation of miRNA and lipids concerning autophagy in therapeutic approaches. The capacity of miRNAs to disrupt various signaling pathways and consequently alter the cellular response and the outcome of diseases is a current hotspot in medical research science (Yang and Wang, 2016), (Butterworth, 2018), (Barbu et al., 2020), (Gorabi et al., 2020), (Gholamrezaei et al., 2020). Gholamrezaei et al. (2020) have studied that the miR-155 inhibitor and mimic effect in L. major-infected macrophages can induce apoptosis and reduce parasite burden and hence highlighting it as an essential biomolecule that may be utilized as a therapeutic target against the disease. However, Taganov et al. (2006) have suggested that induction of miR-146a/b is triggered by those TLRs that mainly sense viral nucleic acids and localize in the intracellular area such as TLR2, TLR4, and TLR5 and proposed a role of a miR-146 in control of TLR and cytokine signaling through a negative feedback regulation loop involving downregulation of IRAK1 and TRAF6 protein levels. Pauley et al. (2010) have shown that the production of 5 cytokines/chemokines (IL-6, IP-10, IL-8, MCP-1, and IL-1b) was reduced after transfection of miR-146a mimic. Thus, it is demonstrated that miR-146a controls acute inflammation caused by LPS stimulation by limiting the production of cytokines after the initial innate response. O’Connell et al. (2007) Findings imply that the JNK pathway, which activates the AP-1 complex, is involved in miR-155 induction by both TLRs and TNF-α, presumably through transcriptional activation of the miR155 encoding BIC gene. Members of the let-7 family of miRNAs are well-represented in the data set in the study by Geraci et al. (2015). Most noticeable are the let-7a and let-7b dichotomous expression patterns, where only DCs and MPs infected with L. donovani display upregulation of those miRNAs, and cells infected with L. major were observed to downregulate the same miRNA (Geraci et al., 2015). For VL (Singh et al., 2016), results confirm that BECN1 is a potential target of MIR30A-3p in both THP-1 cells and HsMDMs infected with L. donovani. Di Loria et al. (2020) have studied that Leishmania organisms can disrupt the production of miR122, which will disrupt the metabolism of cholesterol and ensure its proliferation in the infected host, emphasizing its capacity to hamper lipid metabolism of the host.

The review clarifies that the invading pathogen’s main targets for modulating and maintaining infection in the host are the post-transcriptional and post-translational stages, miRNAs are significant contenders for considering their role in lipid-mediated autophagy.

While it is important to control autophagy brought on by infection to manage parasite survival, it is also important to pay attention to proteins that may serve as targets for autophagy in parasites. Numerous research studies attempt to uncover proteins or chemicals that might impair parasite diversity, infectiousness, or survival.

Unsatisfactory leishmaniasis treatment encourages researchers to investigate more modern options, which now target the parasite’s functioning proteins or molecules. The heat shock protein 90 (Hsp90) is believed to be a commendable drug target against parasitic diseases (Debnath et al., 2014), (Stofberg et al., 2021), (O. Angel et al., 2013), (Silva et al., 2013), (De Andrade et al., 1992). 17-N-allylamino-17-demethoxygeldanamycin (17-AAG), a Hsp90 inhibitor, caused a leishmanicidal effect in vitro (Petersen et al., 2012) and in vivo (Santos et al., 2014) in leishmaniasis. In promastigotes, 17-AAG induces an autophagy pathway, leading to parasite death. Following treatment with 17-AAG, ∆atg5 parasites are less prone to cell death, which shows that autophagy is involved in inhibitor-induced parasite death, where ATG5 is playing an important role (Petersen et al., 2021).

Transporter proteins of the ABC subfamily, LABCG2, are essential for Leishmania virulence (Campos-Salinas et al., 2013). It is necessary for the externalization of phosphatidylserine, a macrophage invasion adaptation strategy. Additionally, it was shown that LABCG1 was a crucial component, cooperating with LABCG2 to control metacyclogenesis, infectivity, oxidative stress, and autophagy (Manzano et al., 2017). Studies on this transporter’s mutations showed that the parasite’s pathogenesis and virulence were both reduced. As a result, these transporters may be exploited as therapeutic targets, and in combination with them, it may be possible to overcome drug resistance (Kabra et al., 2020).

Natural indoloquinoline alkaloid cryptolepine (CLP) induces cellular dysfunction in L. donovani promastigotes, which leads to the contribution of initial autophagic response by showing monodansylcadaverine (MDC)-labeled autophagic vacuoles. However, cells later exhibit characteristics of cell death which may not be because of autophagy but due to prolonged intracellular stress due to CLP (Sengupta et al., 2011). The toxicity of quinoline derivative salts (QDS) was evaluated in mammalian cells, and the mechanism of action proved it as a promising compound (Calixto et al., 2018), while the in vivo effect of the qunoline derivative (AMQ-j) in BALB/c mice was evaluated (Antinarelli et al., 2018). QDS highlighted the anti-leishmanial impact of this substance by inhibiting the formation of autophagic vacuoles, which may have contributed to parasite death by impeding autophagic mechanisms in the clearance of damaged organelles. Additionally, an increase in ROS levels was observed, reinforcing that the induction of oxidative stress triggered the death of intracellular parasites (Calixto et al., 2018). On the other hand, the quinoline derivative (AMQ-j) exhibited several morphological and biochemical changes caused by AMQ-j, including intense mitochondrial swelling, collapse of the mitochondrial membrane potential, abnormal chromatin condensation, externalization of phosphatidylserine, accumulation of lipid bodies, disruption of the cell cycle, formation of autophagic vacuoles, and increase in acidic compartments (Antinarelli et al., 2018). These changes could be related to both QDS and AMQ-j and show a strong effect of autophagy-related and apoptosis-like processes against L. amazonensis and its anti-leishmanial activity (Calixto et al., 2018), (Antinarelli et al., 2018). Thiosemicarbazone molecule (BZTS) in synergy with the available drug miltefosine shows a significant increase in reactive oxygen and nitrogen species as a result of mitochondrial malfunction, leading to severe cell damage, an extensive autophagic process, and the ensuing apoptotic cell death in parasites by least damaging mammalian cells.

Thus, these findings support the synergetic impact on several metabolic pathways in leishmaniasis and encourage the notion of therapeutics toward metabolic pathways and further target identification (Scariot et al., 2017). Anti-leishmanial activity of apigenin in vitro and in vivo was described. Apigenin induced reactive oxygen species (ROS) generation, and the number of autophagosomes after the infection is suggestive of the involvement of host autophagy in macrophages infected with L. amazonensis (Fonseca-Silva et al., 2016). The role of ATG8 in L. donovani for its survival mechanism and infectivity showed it as a drug target. Molecular docking and molecular dynamic simulation studies show the enticing role of thiabendazole derivatives that impede the survival mechanisms by affecting ATG8 (Guhe et al., 2022), while virtual screening of natural ligand library had been performed against ATG8 of L. donovani, showing that urolithin-A which is formed by combinations of coumarin and isocoumarin stably blocked ATG8 (Rahman et al., 2022).

The attention of phenomenal research in leishmaniasis toward therapeutics considering limitations of current treatments is shifting toward autophagy. Targets identified in the Leishmania parasite and respective drugs are enlisted in Table 2. However, there is also a need for a novel approach due to the intricacy of the autophagy network, its connections to other metabolic pathways in the host, and homological conflicts between the presence of autophagy in the host and parasite. Given the complexity of the Leishmania–host relationship, further studies should concentrate on the genetic investigation of autophagic pathway alteration.

The enormous growth in genomic data for pathogens, particularly the available genome sequence, has created a capacity to discover potential vaccines or chemotherapeutic targets. Strategies to accomplish clinical objectives have been made clear by the advent of functional genomics techniques, such as microarray and more recently deep sequencing technologies, as well as proteomics (Meissner et al., 2022). For instance, the proteomic technique is utilized for identifying the binding proteins for a given small molecule. Due to its arduousness and length, this strategy has not been very effective in identifying targets (Ivens et al., 2005). Additionally, in the post-genomic timeframe, these advancements enabled bioinformatics to arise, significantly accelerating the research process. A variety of confirmatory assays, computational algorithms, and high-throughput screening techniques all considerably aid in the identification and characterization of emerging, powerful drug targets (Tao et al., 2004), (Tang et al., 2006). In addition, several computational (in silico) technologies have also been designed.

In diseases caused by external pathogens like bacteria, viruses, and parasites, a comparative functional genomics from humans to the respective pathogen is found to be crucial for identification of novel targets (García-Lara et al., 2005). Genome availability is a key regulator when genetic techniques and bioinformatics approaches are taken into consideration for the understanding of the system. In the post-genomic era, genome information of various pathogens was deciphered, including Leishmania (Ivens et al., 2005), disclosing the haploid genome of L. major (Friedlin strain), where genes involved in host–pathogen interactions were highlighted. Based on the annotation released by the Wellcome Trust Sanger Institute and the genomic sequence of L. major (v5.2), the LeishCyc database was originally developed. LeishCyc is a platform for the analysis, interpretation, and visualization of Leishmania omics data (transcriptomics, proteomics, and metabolomics) in the context of metabolic pathways and offers a systematic approach to structuring the increasing information regarding Leishmania biochemical networks (Doyle et al., 2009). After the post-genomic era, various studies switched to computational approaches for discovering new drug targets as genomic data are available for Leishmania as well. Target-based drug development methods that block a single target molecule hardly ever produce the desired results, but bioinformatics approaches provided a ray of hope for this hypothesis (Schreiber et al., 2016).

A fascinating field called synthetic biology emerged at the beginning of this century. It builds genetic programming systems for desired cellular behavior using molecular biology tools and advanced engineering ideas (Cameron et al., 2014). The goal is to replicate emergent biological processes using synthetic chemicals to develop artificial life. The other goals involve assembling systems with abnormal behavior using replaceable components from natural biology.

The term “synthetic biology” was introduced by Eric Kool and other speakers at the American Chemical Society’s annual meeting in San Francisco in 2000 (Benner and Sismour, 2005). Synthetic biology aims to expand the range of potential biological functions for therapeutic and scientific applications by making biology more efficient, dependable, and predictable to construct. By altering, recombining, and synthesizing wholly new genetic components, synthetic biologists rewire biological systems. This strategy is now feasible because there are more genetic building pieces available and we have a better grasp of how to assemble bimolecular modules, such as protein interaction networks and DNA regulatory sequences. The use of synthetic biology also benefits from developments in mathematical modeling and from engineering-related principles (Endy, 2005). Very few recent pieces of evidence are published that included autophagy modulation via genetic or synthetic circuits (Dey and Rangarajan, 2021), (Gupta et al., 2020). Literature also envisions the importance of the synthetic circuit in developing a leishmaniasis treatment plan (Mol et al., 2014), (Soni and Singh, 2022). There is still opportunity for research and the creation of new strategies for treating the disease by targeting the autophagic processes because, as far as we are aware, there are no studies that describe an autophagy regulation-based synthetic circuit in leishmaniasis.

A less explored and cardinal area in leishmanial infection is lipid metabolism, and it has become the focus nowadays showing its relationship with the autophagy process. The process of autophagy has been a key topic of research due to the intricate mechanism in many biological processes and diseases, because it is still a mystery with many unsolved issues, just like in leishmaniasis. The best methods to find these components might be systems biology-based ones. These methods can be used to gain a thorough understanding of the relationship and operation between lipids, miRNA, and autophagy. This study aims to highlight the interactions between essential biomolecules including RNA, proteins, and lipids that help maintain homeostasis and proper functioning of the cellular process of autophagy and also to identify novel strategies for the treatment of critical elements associated with these three key proteins for autophagy. Recent research on the function of autophagy in leishmaniasis and how it affects parasite survival has been widely disseminated, highlighting the growing significance of this process. The role of several biomolecules, including lipids, proteins, and mRNA, particularly miRNA, in modifying the autophagy process is another research focus. Recently, different ATG proteins such as LC3B, ATG9, ATG5, and ATG7 and other signaling molecules such as mTOR, FOXO, PI3K, and PDL have been shown to play a role in autophagy regulation in infection conditions. Study of autophagy in leishmaniasis is giving more attention to the PI3K/AKT pathway, PERK/ATF4 signaling, and FOXO1/SIRT1 axis. Moreover, LABCG2, an ABC family transporter; HSP90; ATG5; and an ATG8 homolog in Leishmania are a few more targets that have been found important for understanding leishmaniasis in experimental studies (Table 4).

However, there is very little computational research compared to experimental studies. The review encourages filling these gaps to gain a better understanding of the dynamics of the autophagy pathways and their regulation in leishmaniasis. The literature has described the use of a variety of computational techniques in systems biology, including models based on mathematical modeling, AI-based approaches, synthetic biology-based techniques, genetic techniques, and image-based modeling, among many others. However, these techniques have not been sufficiently studied concerning leishmaniasis.

From the perspective of systems biology analysis, a handful of literature reported on autophagy under Leishmania infection. Such a study will help decipher the change in behavior of autophagy and its impact on parasites and help identify potential drug targets against disease. A structure-based study can be performed to determine the possible binding sites of the targets. The identification of binding sites of a protein can help in the rational designing of the therapeutic agents, which could be used to target processes by synthetic biology approaches via genetic circuits. This review also facilitates mathematical modeling to check the robustness of the network and for the identification of important nodes. A pipeline-based study is required in leishmaniasis for targeting the autophagic process and will surely aid to deliver fruitful insights into the role of autophagy in leishmaniasis and its impact on the proliferation and progression of the disease.

The need for new therapeutics against leishmaniasis is driven by the toxicity and drug resistance limitations of currently used chemotherapeutics. In leishmaniasis, it is unclear whether autophagy plays a role in disease progression or regression. Autophagy is a fundamental biological process that eliminates unwanted cellular components and pathogens in order to maintain cellular homeostasis. Due to its significant influence on cellular fate, autophagy is still dominating many cellular processes and signaling networks. Monitoring of genes involved in autophagy and signals that control autophagy have been used to identify and manage the autophagic pathways, and any disruption to any of them may result in several diseases. Given the complexity of autophagy and immunological signaling in disease systems and the growing attention to autophagy research in leishmaniasis, synthetic techniques may prove to be a successful therapeutic approach to cure leishmaniasis. Following many years of research, the experimental evidence on autophagy has grown, creating a thin-line intersection between lipids, proteins, and miRNA for the regulation of autophagy that needs to be investigated. Application of computational biology tools to these datasets may help in understanding information on the crucial proteins that regulate the autophagic processes and their underlying dynamics, which may significantly advance ongoing leishmaniasis research on its therapeutics. In conclusion, our study contributed to the advancement of autophagy research and showed how important biomolecules including lipids, proteins, and miRNA regulate this process. We advocate that in leishmaniasis, computational system biology tools may lead to a promising therapeutic approach for finding newer treatment regimens in the autophagic processes mediated by lipid, protein, and miRNAs.