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Computer-Aided Drug Design Modeling & Simulation Lab

Research Overview

1. Membrane-facilitated molecular recognition

Unraveling Structure-Membrane Interaction Relationships (SMIRs) to Optimize Ligand Access and Binding Kinetics to Membrane-Associated Proteins

The majority of clinically important drug targets in humans are either integral or peripheral membrane-bound proteins that include G protein-coupled receptors (GPCRs), ion channels, cytochrome P450 enzymes, and transporters. Partitioning of drugs within the plasma membrane or membranes of subcellular organelles is known to affect their interactions with such membrane-bound proteins, influencing their efficacy and fate in the body. While membrane interactions can improve efficacy, selectivity, and pharmacokinetic profile, merely increasing drug lipophilicity to increase potency for membrane-associated targets is often detrimental in terms of the overall drug profile. Thus, knowledge of quantitative membrane distribution, preferred location (depth), orientation, and conformation of a drug molecule within the bilayer is crucial in understanding its target binding kinetics, onset and duration of drug action, and disposition. Our central hypothesis, formulated based on extensive literature and our preliminary data, is that mechanistic understanding of the structure-membrane interaction relationship (SMIR) of drug candidates and application of this knowledge to lead optimization will result in improved efficacy, selectivity, safety and disposition.

For more details on this topic, please read our review article on how the cell membrane affects ligand binding to GPCRS (Molecular Pharmacology, 2019) .

2. Outside-in activation of integrins by oxysterols


In collaboration with Dr. Bose laboratory, we recently demonstrated that an oxysterol, 25-hydroxycholesterol (25HC) directly binds to integrins and activates FAK signaling pathway and induces proinflammatory response (Nature Communications, 2019).

Outside-in activation of integrins by 25-hydroxycholesterol

Integrins are noncovalently bonded heterodimeric membrane proteins that play a crucial role in mediating cell-cell interactions, bidirectional signaling across the membrane, cell adhesion and extracellular matrix (ECM) assembly. Integrins bind to a plethora of extracellular ligands that are mainly constituents of ECM and cell adhesion. It has been recently suggested that an oxysterol plays an important role in intensifying pro-inflammatory response following viral (human respiratory syncytial and influenza A) infections, possibly through interaction with cell surface integrins. Activation of Pattern Recognition Receptors (PRRs) is critical for triggering innate immunity and inflammation during infection. The studied oxysterol released from PPR-activated cells is postulated to act as an extracellular soluble mediator to activate oxysterol — integrins (αVβ3 and α5β1) — FAK (focal adhesion kinase) —NFkB pathway for optimal pro-inflammatory response. Our in silico study investigated the molecular recognition of integrins αVβ3 and α5β1  by the oxysterol – by using molecular docking and molecular dynamics simulation techniques. The results revealed that the oxysterol binds to the ectodomain at a site (site II) which is different from the classical ‘RGD’ binding site, makes strong polar and hydrophobic interactions , and triggers significant conformational changes at the “specificity determining loop” of βI domain,  possibly altering ligand binding processes and/or direct integrin activation. Further studies using surface plasmon resonance and radioligand binding assay confirmed  site II as binding site of 25HC. This seemingly druggable binding site opens up new opportunities for small molecule discovery to treat inflammation.

3. Ligand- and Structure-Based Drug Design

Succinic semialdehyde dehydrogenase deficiency (SSADHD)


Our lab utilizes state-of-the-art computational techniques to design and develop small molecule therapeutics for orphan diseases. In collaboration with Dr. Gibson, we have embarked on identifying high affinity ligands for gamma-hydroxy butyric acid (GHB) receptors.

Succinic semialdehyde dehydrogenase deficiency (SSADHD), though an ultra-rare disease (diagnosed in ~200 patients worldwide), is the most prevalent inherited disorder of GABA metabolism. The disease presents with non-specific mild to moderate developmental delay, severe expressive language impairment , epilepsy, and neuropsychiatric problems. Functional deficiency of SSADH prevents the conversion of succinic semialdehyde to succinic acid, resulting in excessive accumulation of neurotransmitters g-aminobutyric acid (GABA) and the GABA analogue g-hydroxybutyrate (GHB), and use-dependent down-regulation of GABA and GHB receptors. Blocking GHB receptors with specific antagonists has been shown to rescue SSADH-deficient mice from premature lethality and may provide therapeutic benefits to patients with SSADHD. In the absence of biophysical and structural information of the GHB receptor, a ligand-based pharmacophore-modeling and virtual screening strategy is being implemented to find high-affinity small molecules with potential GHB receptor antagonist activity.