Computational Characterization of Binding of Small Molecule Inhibitors to HIV-1 gp41

Sphingolipid metabolism is tightly controlled by enzymes to regulate essential processes such as energy utilisation and cell proliferation. The central metabolite is ceramide, a pro-apoptotic lipid catabolized by ceramidase enzymes to ultimately produce pro-proliferative sphingosine-1-phosphate. Human ceramidases can be soluble proteins (acid and neutral ceramidase) or integral membrane proteins (alkaline ceramidases). Increasing ceramide levels to increase apoptosis has shown efficacy as a cancer treatment using small molecules inhibiting a soluble ceramidase. Due to the transmembrane nature of alkaline ceramidases, no specific small molecule inhibitors have been reported. Here, we report novel fluorescent substrates (FRETceramides) of ceramidases that can be used to monitor enzyme activity in real-time. We use FRETceramides to discover the first drug-like inhibitors of alkaline ceramidase 3 (ACER3) which are active in cell-based assays. Biophysical characterization of enzyme:inhibitor interactions reveal a new paradigm for inhibition of lipid metabolising enzymes with non-lipidic small molecules.

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Faculty Opinions recommendation of Characterization of two classes of small molecule inhibitors of Arp2/3 complex.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1163364.861078 ◽

2010 ◽

Author(s):

David G Oppenheimer

Keyword(s):

Small Molecule ◽

Small Molecule Inhibitors

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Preclinical Characterization of Signal Transducer and Activator of Transcription 3 Small Molecule Inhibitors for Primary and Metastatic Brain Cancer Therapy

Journal of Pharmacology and Experimental Therapeutics ◽

10.1124/jpet.114.214619 ◽

2014 ◽

Vol 349 (3) ◽

pp. 458-469 ◽

Cited By ~ 22

Author(s):

Hikmat H. Assi ◽

Chris Paran ◽

Nathan VanderVeen ◽

Jonathan Savakus ◽

Robert Doherty ◽

...

Keyword(s):

Cancer Therapy ◽

Small Molecule ◽

Brain Cancer ◽

Small Molecule Inhibitors ◽

Signal Transducer ◽

Transcription 3

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Identification and characterization of benzo[d]oxazol-2(3H)-one derivatives as the first potent and selective small-molecule inhibitors of chromodomain protein CDYL

European Journal of Medicinal Chemistry ◽

10.1016/j.ejmech.2019.111656 ◽

2019 ◽

Vol 182 ◽

pp. 111656 ◽

Cited By ~ 3

Author(s):

Lixin Yang ◽

Yongqing Liu ◽

Minghua Fan ◽

Guiwang Zhu ◽

Hongwei Jin ◽

...

Keyword(s):

Small Molecule ◽

Small Molecule Inhibitors ◽

Identification And Characterization

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Release of gp120 Restraints Leads to an Entry-Competent Intermediate State of the HIV-1 Envelope Glycoproteins

mBio ◽

10.1128/mbio.01598-16 ◽

2016 ◽

Vol 7 (5) ◽

Cited By ~ 59

Author(s):

Alon Herschhorn ◽

Xiaochu Ma ◽

Christopher Gu ◽

John D. Ventura ◽

Luis Castillo-Menendez ◽

...

Keyword(s):

Small Molecule ◽

Intermediate State ◽

Neutralizing Antibodies ◽

Small Molecule Inhibitors ◽

Virus Entry ◽

Envelope Glycoproteins ◽

Low Levels ◽

State 1 ◽

Hiv 1 ◽

Conformation State

ABSTRACTPrimary human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimers [(gp120/gp41)3] typically exist in a metastable closed conformation (state 1). Binding the CD4 receptor triggers Env to undergo extensive conformational changes to mediate virus entry. We identified specific gp120 residues that restrain Env in state 1. Alteration of these restraining residues destabilized state 1, allowing Env to populate a functional conformation (state 2) intermediate between state 1 and the full CD4-bound state (state 3). Increased state 2 occupancy was associated with lower energy barriers between the states. State 2 was an obligate intermediate for all transitions between state 1 and state 3. State 2-enriched Envs required lower CD4 concentrations to trigger virus entry and more efficiently infected cells expressing low levels of CD4. These Envs were resistant to several broadly neutralizing antibodies and small-molecule inhibitors. Thus, state 2 is an Env conformation on the virus entry pathway; sampling state 2 increases the adaptability of HIV-1 to different host cell receptor levels and immune environments. Our results provide new insights into the conformational regulation of HIV-1 entry.IMPORTANCEThe envelope glycoproteins (Env) of HIV-1 mediate virus entry and are the sole targets of neutralizing antibodies. Understanding the way that Env promotes HIV-1 entry can expedite drug and vaccine development. By destabilizing Env, we found that it assumes an intermediate state that is functional and obligate for transitions to entry-competent conformations. Increased sampling of this state enhances the ability of HIV-1 to infect cells that express low levels of the CD4 receptor and allows the virus to evade neutralizing antibodies and small-molecule inhibitors. These findings provide new mechanistic insights into the function and inhibition of HIV-1 Env and will contribute to ongoing therapeutic and prevention efforts to combat HIV-1.

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