Farah Ammar - Academia.edu (original) (raw)
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Papers by Farah Ammar
Retrovirology, 2012
HIV integrase (IN) is a privileged target for antiviral treatments. These induce the emergence of... more HIV integrase (IN) is a privileged target for antiviral treatments. These induce the emergence of resistant strains, prompting the search of new drugs. To better understand the relationships between structure and function of IN and identify new anti-HIV inhibitors we prepared antibodies recognizing the IN a4 helix that binds viral DNA ends and contributes to the integration process and antibodies recognizing a loop in between the a4 and a5 helices which participates to the binding of LEDGF a protein that helps IN to anchor viral DNA.
PLoS ONE, 2012
Integration of HIV DNA into host chromosome requires a 39-processing (39-P) and a strand transfer... more Integration of HIV DNA into host chromosome requires a 39-processing (39-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 39-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 59C 4 pA 3 39 step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance.
Integrase (IN) is the retroviral enzyme that catalyzes integration of viral cDNA into the infecte... more Integrase (IN) is the retroviral enzyme that catalyzes integration of viral cDNA into the infected cell chromosome. Integration involves two steps: the 3' processing (3'P) of viral DNA in the cytoplasm and the strand transfer (ST) in the nucleus. The DKA (diketoacid) related compounds raltegravir (RAL), elvitegravir (EVG) and dolutegravir have been approved recently by the FDA for use in anti-AIDS/HIV therapy. These are effective inhibitors of integration, acting as INSTIs (IN ST inhibitors) at the IN-viral DNA interface. However, in a recent report we have shown that the high affinity binding of RAL to viral LTR (long terminal repeat) ends does not require the presence of the enzyme. Our results suggested that a strong binding to HIV DNA is one of the prerogatives of INSTIs endowed with high antiviral activities (Ammar et al., 2012). To better understand its inhibitory activity on IN we analyzed its binding properties compared with TB11 which is one of the first DKAs synthe...
Retrovirology, 2012
HIV integrase (IN) is a privileged target for antiviral treatments. These induce the emergence of... more HIV integrase (IN) is a privileged target for antiviral treatments. These induce the emergence of resistant strains, prompting the search of new drugs. To better understand the relationships between structure and function of IN and identify new anti-HIV inhibitors we prepared antibodies recognizing the IN a4 helix that binds viral DNA ends and contributes to the integration process and antibodies recognizing a loop in between the a4 and a5 helices which participates to the binding of LEDGF a protein that helps IN to anchor viral DNA.
PLoS ONE, 2012
Integration of HIV DNA into host chromosome requires a 39-processing (39-P) and a strand transfer... more Integration of HIV DNA into host chromosome requires a 39-processing (39-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 39-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 59C 4 pA 3 39 step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance.
Integrase (IN) is the retroviral enzyme that catalyzes integration of viral cDNA into the infecte... more Integrase (IN) is the retroviral enzyme that catalyzes integration of viral cDNA into the infected cell chromosome. Integration involves two steps: the 3' processing (3'P) of viral DNA in the cytoplasm and the strand transfer (ST) in the nucleus. The DKA (diketoacid) related compounds raltegravir (RAL), elvitegravir (EVG) and dolutegravir have been approved recently by the FDA for use in anti-AIDS/HIV therapy. These are effective inhibitors of integration, acting as INSTIs (IN ST inhibitors) at the IN-viral DNA interface. However, in a recent report we have shown that the high affinity binding of RAL to viral LTR (long terminal repeat) ends does not require the presence of the enzyme. Our results suggested that a strong binding to HIV DNA is one of the prerogatives of INSTIs endowed with high antiviral activities (Ammar et al., 2012). To better understand its inhibitory activity on IN we analyzed its binding properties compared with TB11 which is one of the first DKAs synthe...