Neurological disorders (NDs) are usually due to structural and/or functional losses of neurons and eventually neuronal death [1
]. Literally, hundreds of neurological/neurodegenerative diseases have been identified, but some like Alzheimer’s disease (AD) and Parkinson’s disease (PD) are very well known and have devastating impacts in modern society. NDs tend to share some characteristics such as memory loss and the aggregation of abnormal proteins [2
]. Neuronal death is the main characteristic of major NDs, and apoptosis is considered a possible mechanism of neuronal death in the majority of NDs [3
]. Furthermore, abnormal or excessive neuron apoptosis eventually lead to a number of incurable diseases including AD, PD, Huntington’s disease (HD), and stroke [4
]. The genes that crucially contribute to AD (β-amyloid precursor protein (APP), and presenilin-1 and -2) have been demonstrated to regulate apoptosis, which intimates dysregulation of apoptosis plays a notable role in triggering the neuronal loss in AD [6
Caspases are the main executioners of apoptosis and are usually proteolytic in nature [7
]. Caspases constitute a distinctive set of proteases (cysteine aspartate-specific) with the specific substrate and biological functions [8
]. They are categorized as ‘inflammatory’ or ‘apoptotic’ on the basis of their functions and pro-domain structures and may further be categorized as initiator (caspase 2, 8, 9, and 10) or effector caspases (caspase 3, 6, and caspase 7) [10
]. Caspases have been identified in the brains of AD patients, and caspases 1, 2, 3, 5, 6, 7, 8 and 9 have all been reported to be transcriptionally up-regulated in AD [12
]. Several studies, including neuropathologic and clinical imaging observations, indicate that stimulated microglia (the monocyte-derived macrophage-like resident immune cells of the central nervous system) are primarily responsible for the pathogeneses of a number of NDs, including AD, PD, and multiple sclerosis [13
]. Activated microglia release neurotoxic pro-inflammatory factors [16
], and accumulated evidence indicates caspases (especially, caspase 3/7 and caspase 8) are key regulators of microglial activation [14
]. Furthermore, neuroinflammation in the brains of AD and PD patients is attributed to the presence of activated microglia [15
]. Thus, it has been suggested the identification of potent caspase inhibitors might prove to be a potent strategy for identifying neuroprotective agents for the treatment of several NDs [18
Caspase 8 is involved in apoptosis and cytokine processing. The latter represents an initial step of the apoptotic cascade, which initiates proteolytic stimulation of downstream caspases and proceeds to apoptosis [20
]. Activated caspase 8 has been detected in the AD brain, and its activation has been posited to be due to the stimulation of receptors in the ‘death-receptor pathway’ [21
]. Furthermore, the stimulation of caspase 8 in activated microglia prevents their committing to necroptosis. Consequently, the identification of effective caspase 8 inhibitors might protect neurons by selectively killing or blocking the activities of activated microglia [22
Activated caspase 8 has been detected within insoluble elements in HD brains [24
], and reported to be significantly up-regulated in cerebrospinal fluid in amyotrophic lateral sclerosis (ALS) [25
]. In addition, activated caspase 8 levels are significantly elevated in patients suffering from Dentatorubralpallidoluysian atrophy (DRPLA), a rare ND with a genetic pathology of polyglutamine (CAG) repeats [23
]. In this study, we applied state of art in silico approaches, that is, pharmacophore modeling, virtual screening, molecular dynamics, molecular docking simulations, and MM-PBSA analysis in an attempt to discover potential caspase 8 inhibitors.
Common feature-based pharmacophore modelling and structure-based docking study were applied to identify novel caspase 8 inhibitors. A pharmacophore model (Hypo-1) was developed and validated and used as a filtering tool to screen the ZINC database. After a series of screenings followed by visual inspection and molecular docking of selected compounds, the two most potent compounds were subjected to molecular docking with caspase 8 at different time intervals (0 ns, 5 ns, 10 ns, 15 ns, and 20 ns) to obtain deeper insight of their binding efficacies.
The binding free energies of these two compounds were comparable or better than those of previously described caspase 8 inhibitors and satisfied most drug candidate criteria. Using a combination of pharmacophore modeling, virtual screening, molecular docking, and finally molecular dynamics simulations of these two proteins at different time intervals and their binding affinities, we conclude that ZINC19370490 and ZINC04534268 be viewed as potential lead compounds.