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1.
Protein Sci ; 32(12): e4814, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37861472

ABSTRACT

HIV-1 reverse transcriptase (RT) remains a key target for HIV drug development. As successful management of the disease requires lifelong treatment, the emergence of resistance mutations is inevitable, making development of new RT inhibitors, which remain effective against resistant variants crucial. To this end, previous computationally guided drug design efforts have resulted in catechol diether compounds, which inhibit wildtype RT with picomolar affinities and appear to be promising preclinical candidates. To confirm that these compounds remain potent against Y181C, a widespread mutation conferring resistance to first generation inhibitors, they were screened against the HIV-1 N119 clinical isolate, reported as a Y181C single mutant. In comparison to a molecular clone with the same mutation, N119 appears less susceptible to inhibition by our preclinical candidate compounds. A more detailed sequencing effort determined that N119 was misidentified and carries V106A in combination with Y181C. While both indolizine and naphthalene substituted catechol diethers are potent against the classical Y181C single mutant, the addition of V106A confers more resistance against the indolizine derivatives than the naphthalene derivatives. Crystal structures presented in this study highlight key features of the naphthyl group, which allow these compounds to remain potent in the double mutant, including stronger interactions with F227 and less reliance on V106 for stabilization of the ethoxy-uracil ring, which makes critical hydrogen bonds with other residues in the binding pocket.


Subject(s)
Anti-HIV Agents , HIV-1 , Indolizines , Reverse Transcriptase Inhibitors/pharmacology , Reverse Transcriptase Inhibitors/chemistry , HIV Reverse Transcriptase/chemistry , Indolizines/pharmacology , Catechols/chemistry , Catechols/pharmacology , Naphthalenes/pharmacology , Anti-HIV Agents/pharmacology , Anti-HIV Agents/chemistry , Structure-Activity Relationship
2.
PLoS Negl Trop Dis ; 17(4): e0011303, 2023 04.
Article in English | MEDLINE | ID: mdl-37104530

ABSTRACT

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.


Subject(s)
Elephantiasis, Filarial , Folic Acid Antagonists , Animals , Folic Acid Antagonists/pharmacology , Folic Acid Antagonists/metabolism , Wuchereria bancrofti , Folic Acid , Tetrahydrofolate Dehydrogenase/metabolism , NADP , Molecular Docking Simulation
3.
Front Mol Biosci ; 9: 805187, 2022.
Article in English | MEDLINE | ID: mdl-35237658

ABSTRACT

Reverse transcriptase (RT) from the human immunodeficiency virus continues to be an attractive drug target for antiretroviral therapy. June 2022 will commemorate the 30th anniversary of the first Human Immunodeficiency Virus (HIV) RT crystal structure complex that was solved with non-nucleoside reverse transcriptase inhibitor nevirapine. The release of this structure opened opportunities for designing many families of non-nucleoside reverse transcriptase inhibitors (NNRTIs). In paying tribute to the first RT-nevirapine structure, we have developed several compound classes targeting the non-nucleoside inhibitor binding pocket of HIV RT. Extensive analysis of crystal structures of RT in complex with the compounds informed iterations of structure-based drug design. Structures of seven additional complexes were determined and analyzed to summarize key interactions with residues in the non-nucleoside inhibitor binding pocket (NNIBP) of RT. Additional insights comparing structures with antiviral data and results from molecular dynamics simulations elucidate key interactions and dynamics between the nucleotide and non-nucleoside binding sites.

4.
Ann Pharmacother ; 55(10): 1290-1296, 2021 10.
Article in English | MEDLINE | ID: mdl-33533262

ABSTRACT

OBJECTIVE: To review the efficacy and safety of clascoterone 1% cream for the treatment of acne vulgaris in patients 12 years of age and older. DATA SOURCES: A literature search through PubMed, MEDLINE, and ClinicalTrials.gov was conducted using the following keywords: clascoterone, cream, acne, and CB-03-01. Articles published between 2004 and 2020 were included in this review. STUDY SELECTION AND DATA EXTRACTION: Preclinical and clinical studies describing the efficacy and safety of topical clascoterone cream were included. DATA SYNTHESIS: Early preclinical studies demonstrated that clascoterone exhibits local antiandrogenic effects without any systemic effects. Phase 2 and 3 trials demonstrated a statistically significant reduction in inflammatory and noninflammatory lesions and mild erythema with clascoterone use. Long-term studies confirmed the favorable safety profile of the drug in subjects for up to 9 months of use, with erythema being the most common treatment-emergent local skin reaction. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE: Pharmacological treatment options for acne vulgaris include topical and systemic agents. Systemic antiandrogen medications are associated with adverse effects and should be avoided in pregnancy and male patients. Clascoterone is a novel topical antiandrogen drug with no systemic adverse effects. This drug provides prescribers with an appealing treatment option for male and female patients 12 years of age and older, who are not candidates for systemic drugs because of contraindications or adverse effects or who have failed other topical therapies. CONCLUSION: Clascoterone, a novel topical androgen receptor inhibitor, is a safe and effective treatment option for patients with acne vulgaris.


Subject(s)
Acne Vulgaris , Receptors, Androgen , Acne Vulgaris/drug therapy , Cortodoxone/analogs & derivatives , Female , Humans , Male , Propionates , Treatment Outcome
5.
AAPS PharmSciTech ; 21(7): 256, 2020 Sep 04.
Article in English | MEDLINE | ID: mdl-32888114

ABSTRACT

3D printing has been widely used to rapidly manufacture a variety of solid dosage forms on-demand, without sacrificing precision. This study used extrusion-based 3D printing to prepare single-layered, tri-layered, and core-in-shell poly(lactic-co-glycolic acid) (PLGA) films carrying paclitaxel and rapamycin in combination or lidocaine alone. Each layer was composed of either low molecular weight (MW) PLGA or high MW PLGA. In vitro drug release kinetics of paclitaxel, rapamycin, and lidocaine for PLGA films were assessed and compared with PLGA-polyethylene glycol (PEG)-PLGA hydrogel discs. Regardless of the structure of PLGA film, paclitaxel (half-time: 54-63 days) was released faster than when compared with rapamycin (half-time: 74-80 days). In contrast, single-layered PLGA-PEG-PLGA discs released rapamycin (half-time 5.7 h) at a more rapid rate than paclitaxel (half-time: 7.3 h). Single-layered PLGA-PEG-PLGA discs enabled a faster drug release than PLGA films, noting that the disc matrices dissolve in water in 24 h. Similarly, lidocaine incorporated in PLGA films (half-time: 13-36 days) exhibited slower release patterns than that in PLGA-PEG-PLGA discs (half-time: 2.6 h). In vitro drug release patterns were explained using molecular models that simulate drug-polymer interactions. Analysis of models suggested that drug-polymer interactions, location of each drug in the polymeric matrix, and solubility of drugs in water were major factors that determine drug release behaviors from the polymeric films and discs.


Subject(s)
Drug Carriers/chemistry , Drug Delivery Systems , Polylactic Acid-Polyglycolic Acid Copolymer/chemistry , Printing, Three-Dimensional , Antineoplastic Agents, Phytogenic/administration & dosage , Humans , Molecular Weight , Paclitaxel/administration & dosage , Solubility
6.
Purinergic Signal ; 16(3): 415-426, 2020 09.
Article in English | MEDLINE | ID: mdl-32789792

ABSTRACT

Animal models of asthma have shown that limonene, a naturally occurring terpene in citrus fruits, can reduce inflammation and airway reactivity. However, the mechanism of these effects is unknown. We first performed computational and molecular docking analyses that showed limonene could bind to both A2A and A2B receptors. The pharmacological studies were carried out with A2A adenosine receptor knock-out (A2AKO) and wild-type (WT) mice using ovalbumin (OVA) to generate the asthma phenotype. We investigated the effects of limonene on lung inflammation and airway responsiveness to methacholine (MCh) and NECA (nonselective adenosine analog) by administering limonene as an inhalation prior to OVA aerosol challenges in one group of allergic mice for both WT and KO. In whole-body plethysmography studies, we observed that airway responsiveness to MCh in WT SEN group was significantly lowered upon limonene treatment but no effect was observed in A2AKO. Limonene also attenuated NECA-induced airway responsiveness in WT allergic mice with no effect being observed in A2AKO groups. Differential BAL analysis showed that limonene reduced levels of eosinophils in allergic WT mice but not in A2AKO. However, limonene reduced neutrophils in sensitized A2AKO mice, suggesting that it may activate A2B receptors as well. These data indicate that limonene-induced reduction in airway inflammation and airway reactivity occurs mainly via activation of A2AAR but A2B receptors may also play a supporting role.


Subject(s)
Asthma/drug therapy , Inflammation/drug therapy , Limonene/pharmacology , Receptor, Adenosine A2A/metabolism , Animals , Asthma/chemically induced , Asthma/metabolism , Disease Models, Animal , Inflammation/chemically induced , Inflammation/metabolism , Limonene/therapeutic use , Lung/drug effects , Lung/metabolism , Mice , Mice, Transgenic , Ovalbumin , Receptor, Adenosine A2A/genetics
7.
Curr HIV Res ; 18(4): 283-291, 2020.
Article in English | MEDLINE | ID: mdl-32493197

ABSTRACT

BACKGROUND: Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are used in combination with antiretroviral therapy to suppress viral loads in HIV patients. The chemical design of NNRTIs has changed in recent years in response to resistance-associated mutations (RAMs) and resistance. NNRTIs are chemically diverse compounds that bind an allosteric site of HIV RT. Resistance- associated mutations (RAMs) identified in HIV patients are associated with NNRTI resistance. RAMs confer amino acid changes that alter both structural and physiochemical properties of the allosteric site. Ultimately, these changes reduce NNRTI affinity. Previously, we used a combination of computational and experimental methods to analyze and validate RAMs for 3 diarylpyrimidine (DAPY) NNRTIs. OBJECTIVE: The objective of this study is to apply these methods to other chemically diverse, non- DAPY NNRTIs. MATERIALS AND METHODS: We selected MIV-150 (experimental microbicide) and doravirine for this study. A computational and molecular modeling strategy was used to evaluate the effects of RAMs. Calculated changes in drug affinity and stability (ΔS + ΔA) were used to determine overall resistance levels: susceptible, low, intermediate, and high. The ΔS + ΔA values for K101P suggest that this mutation confers intermediate/high-level resistance to MIV-150, but remains susceptible to doravirine. Based on the determined resistance levels, we analyzed the models and used Molecular Dynamics (MD) to compare the interactions of MIV-150/doravirine with RT wild-type (WT) and RT (K101P). From MD, we found that key interactions were lost with RT (K101P), but were retained with doravirine. To experimentally validate our findings, we conducted a fluorescence-based reverse transcription assay for MIV-150 with RT (WT) and RT (K101P). IC50 values determined in assays showed a 101-fold change in potency for MIV-150, but essentially no change for doravirine. RESULTS: Our computational and experimental results are also consistent with antiviral data reported in the literature. CONCLUSION: We believe that this approach is effective for analyzing mutations to determine resistance profiles for chemically diverse NNRTIs in development.


Subject(s)
Anti-HIV Agents/pharmacology , HIV Reverse Transcriptase/genetics , HIV-1/drug effects , Mutation , Pyridines/pharmacology , Pyridones/pharmacology , Reverse Transcriptase Inhibitors/pharmacology , Triazoles/pharmacology , Urea/analogs & derivatives , Allosteric Site , Anti-HIV Agents/chemistry , Binding Sites , Drug Resistance, Viral/genetics , Enzyme Assays , Gene Expression , HIV Infections/drug therapy , HIV Reverse Transcriptase/antagonists & inhibitors , HIV Reverse Transcriptase/chemistry , HIV Reverse Transcriptase/metabolism , HIV-1/enzymology , HIV-1/genetics , Humans , Kinetics , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Pyridines/chemistry , Pyridones/chemistry , Reverse Transcriptase Inhibitors/chemistry , Structure-Activity Relationship , Thermodynamics , Triazoles/chemistry , Urea/chemistry , Urea/pharmacology
8.
Curr Pharm Teach Learn ; 12(3): 339-346, 2020 03.
Article in English | MEDLINE | ID: mdl-32273073

ABSTRACT

BACKGROUND AND PURPOSE: Courses that integrate pharmacology, medicinal chemistry, and pharmacotherapy are widely implemented in pharmacy curriculums. The integration of medicinal chemistry is often challenging given the difficulty of material and time constraints. The objective of this pedagogical approach is to utilize structure activity relationship (SAR) maps as visual aids to teach students medicinal chemistry in an integrated course. EDUCATIONAL SETTING: SAR maps were designed and implemented within an integrated course focusing on cardiopulmonary diseases. Specific SAR maps used in lecture and class activities included phenylethylamines (adrenergic agonists (i.e. bronchodilators)) and aryloxypropanolamines (beta blockers). Students were assessed in class activities (formative) and exams (high stakes) for specific information surrounding drug structure and the SAR map. Drug properties assessed included essential pharmacophores, pharmacodynamics, physiochemical properties, metabolism, duration of action, and decision-making. FINDINGS: Results from assessment item analysis reveal that students performed well on medicinal chemistry questions related to the SAR maps (~90% correct on first exam). Students revealed in a survey that the SAR maps enhanced their understanding of medicinal chemistry concepts. SUMMARY: SAR maps are effective tools that visually teach students key concepts in medicinal chemistry. This millennial student-friendly tool is time-effective and promotes learning as opposed to drug structure memorization. The SAR map can be easily implemented in other integrated courses focused on various disease states.


Subject(s)
Chemistry, Pharmaceutical/education , Chemistry, Pharmaceutical/standards , Drug Therapy/instrumentation , Structure-Activity Relationship , Students/statistics & numerical data , Chemistry, Pharmaceutical/methods , Curriculum/standards , Drug Therapy/methods , Drug Therapy/statistics & numerical data , Humans , Students/psychology , Surveys and Questionnaires
9.
Bioorg Med Chem Lett ; 29(16): 2182-2188, 2019 08 15.
Article in English | MEDLINE | ID: mdl-31281023

ABSTRACT

The development of efficacious NNRTIs for HIV/AIDS therapy is commonly met with the emergence of drug resistant strains, including the Y181C variant. Using a computationally-guided approach, we synthesized the catechol diether series of NNRTIs, which display sub-nanomolar potency in cellular assays. Among the most potent were a series of 2-cyanoindolizine substituted catechol diethers, including Compound 1. We present here a thorough evaluation of this compound, including biochemical, cellular, and structural studies. The compound demonstrates low nanomolar potency against both WT and Y181C HIV-1 RT in in vitro and cellular assays. Our crystal structures of both the wildtype and mutant forms of RT in complex with Compound 1 allow the interrogation of this compound's features that allow it to maintain strong efficacy against the drug resistant mutant. Among these are compensatory shifts in the NNRTI binding pocket, persistence of multiple hydrogen bonds, and van der Waals contacts throughout the binding site. Further, the fluorine at the C6 position of the indolizine moiety makes multiple favorable interactions with both RT forms. The present study highlights the indolizine-substituted catechol diether class of NNRTIs as promising therapeutic candidates possessing optimal pharmacological properties and significant potency against multiple RT variants.


Subject(s)
Anti-HIV Agents/therapeutic use , Catechols/chemistry , HIV Reverse Transcriptase/metabolism , Reverse Transcriptase Inhibitors/therapeutic use , Anti-HIV Agents/pharmacology , Drug Design , Molecular Structure , Reverse Transcriptase Inhibitors/pharmacology
10.
Curr Pharm Teach Learn ; 10(11): 1529-1540, 2018 11.
Article in English | MEDLINE | ID: mdl-30514546

ABSTRACT

BACKGROUND AND PURPOSE: This project investigates the use of pharmacy student metacognitive learning in a laboratory-based science research advanced pharmacy practice experience (APPE). EDUCATIONAL ACTIVITY AND SETTING: We describe a five-week research APPE. This course is separated into two parts which run simultaneously. In part 1, students read and discuss papers from primary literature to learn the context of the project and the theory behind each laboratory procedure. In part 2, students perform experiments in the laboratory that contribute to the primary investigator's (PI's) ongoing research project and relate directly to the readings from part 1. Metacognitive processes allow students to better understand and evaluate the primary literature and to connect that information with the hands-on experiments being performed. FINDINGS: Currently, this APPE has run five times with a total of eight students. Student learning was assessed by several written and oral assignments graded with rubrics. Students' perceptions of their own learning and metacognitive development following the course was assessed using a survey. SUMMARY: This APPE seems to be a useful experience for both faculty and students. Students obtain laboratory and metacognitive skill development, while the collaborating laboratory is supplied with material required for further experiments. Importantly, the APPE preceptor is not the PI, so the preceptor is able to focus on the learning skills (both metacognition and hands-on) portion of the APPE.


Subject(s)
Curriculum/trends , Pharmacy Research/methods , Education, Pharmacy, Graduate/methods , Education, Pharmacy, Graduate/trends , Educational Measurement/methods , Humans , Surveys and Questionnaires
11.
J Mol Graph Model ; 79: 133-139, 2018 01.
Article in English | MEDLINE | ID: mdl-29156381

ABSTRACT

Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) is a leading cause of HIV treatment failure. Often included in antiviral therapy, NNRTIs are chemically diverse compounds that bind an allosteric pocket of enzyme target reverse transcriptase (RT). Several new NNRTIs incorporate flexibility in order to compensate for lost interactions with amino acid conferring mutations in RT. Unfortunately, even successful inhibitors such as diarylpyrimidine (DAPY) inhibitor rilpivirine are affected by mutations in RT that confer resistance. In order to aid drug design efforts, it would be efficient and cost effective to pre-evaluate NNRTI compounds in development using a structure-based computational approach. As proof of concept, we applied a residue scan and molecular dynamics strategy using RT crystal structures to predict mutations that confer resistance to DAPYs rilpivirine, etravirine, and investigational microbicide dapivirine. Our predictive values, changes in affinity and stability, are correlative with fold-resistance data for several RT mutants. Consistent with previous studies, mutation K101P is predicted to confer high-level resistance to DAPYs. These findings were further validated using structural analysis, molecular dynamics, and an enzymatic reverse transcription assay. Our results confirm that changes in affinity and stability for mutant complexes are predictive parameters of resistance as validated by experimental and clinical data. In future work, we believe that this computational approach may be useful to predict resistance mutations for inhibitors in development.


Subject(s)
Diarylquinolines/chemistry , HIV Reverse Transcriptase/chemistry , Quantitative Structure-Activity Relationship , Reverse Transcriptase Inhibitors/chemistry , Diarylquinolines/pharmacology , Drug Design , Drug Resistance, Viral , HIV Reverse Transcriptase/antagonists & inhibitors , HIV Reverse Transcriptase/genetics , Humans , Microbial Sensitivity Tests , Molecular Docking Simulation , Molecular Dynamics Simulation , Mutation , Recombinant Proteins , Reverse Transcriptase Inhibitors/pharmacology
12.
ACS Med Chem Lett ; 6(10): 1075-9, 2015 Oct 08.
Article in English | MEDLINE | ID: mdl-26487915

ABSTRACT

Catechol diether compounds have nanomolar antiviral and enzymatic activity against HIV with reverse transcriptase (RT) variants containing K101P, a mutation that confers high-level resistance to FDA-approved non-nucleoside inhibitors efavirenz and rilpivirine. Kinetic data suggests that RT (K101P) variants are as catalytically fit as wild-type and thus can potentially increase in the viral population as more antiviral regimens include efavirenz or rilpivirine. Comparison of wild-type structures and a new crystal structure of RT (K101P) in complex with a leading compound confirms that the K101P mutation is not a liability for the catechol diethers while suggesting that key interactions are lost with efavirenz and rilpivirine.

13.
Future Microbiol ; 10(11): 1767-72, 2015.
Article in English | MEDLINE | ID: mdl-26517310

ABSTRACT

Resistance continues to emerge as a leading cause for antiretroviral treatment failure. Several mutations in HIV reverse transcriptase (RT) confer resistance to non-nucleoside inhibitors (NNRTIs), vital components of antiretroviral combination therapies. Since the majority of mutations are located in the NNRTI binding pocket, crystal structures of RT variants in complex with NNRTIs have provided ideas for new drug design strategies. This article reviews the impact of RT crystal structures on the multidisciplinary design and development of new inhibitors with improved resistance profiles.


Subject(s)
Anti-HIV Agents/isolation & purification , Anti-HIV Agents/pharmacology , Drug Discovery/methods , HIV Reverse Transcriptase/antagonists & inhibitors , HIV/drug effects , Reverse Transcriptase Inhibitors/isolation & purification , Reverse Transcriptase Inhibitors/pharmacology , Crystallography, X-Ray , Drug Discovery/trends , Drug Resistance, Viral , HIV/enzymology , HIV Reverse Transcriptase/chemistry , Humans , Molecular Docking Simulation , Mutation , Protein Conformation , Selection, Genetic
14.
Bioorg Med Chem Lett ; 25(21): 4824-4827, 2015 Nov 01.
Article in English | MEDLINE | ID: mdl-26166629

ABSTRACT

Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that incorporate a 7-indolizinylamino or 2-naphthylamino substituent on a pyrimidine or 1,3,5-triazine core. The most potent compounds show below 10 nanomolar activity towards wild-type HIV-1 and variants bearing Tyr181Cys and Lys103Asn/Tyr181Cys resistance mutations. The compounds also feature good aqueous solubility. Crystal structures for two complexes enhance the analysis of the structure-activity data.


Subject(s)
Anti-HIV Agents/chemistry , Anti-HIV Agents/pharmacology , Azabicyclo Compounds/pharmacology , Bridged Bicyclo Compounds/pharmacology , Drug Discovery , HIV Reverse Transcriptase/antagonists & inhibitors , HIV/drug effects , Reverse Transcriptase Inhibitors/chemistry , Reverse Transcriptase Inhibitors/pharmacology , Triazines/pharmacology , Anti-HIV Agents/chemical synthesis , Azabicyclo Compounds/chemical synthesis , Azabicyclo Compounds/chemistry , Bridged Bicyclo Compounds/chemical synthesis , Bridged Bicyclo Compounds/chemistry , Cell Line , Cell Proliferation/drug effects , Dose-Response Relationship, Drug , HIV Reverse Transcriptase/metabolism , Humans , Models, Molecular , Molecular Structure , Reverse Transcriptase Inhibitors/chemical synthesis , Solubility , Structure-Activity Relationship , Triazines/chemical synthesis , Triazines/chemistry
15.
J Med Chem ; 58(6): 2737-45, 2015 Mar 26.
Article in English | MEDLINE | ID: mdl-25700160

ABSTRACT

The development of novel non-nucleoside inhibitors (NNRTIs) with activity against variants of HIV reverse transcriptase (RT) is crucial for overcoming treatment failure. The NNRTIs bind in an allosteric pocket in RT ∼10 Å away from the active site. Earlier analogues of the catechol diether compound series have picomolar activity against HIV strains with wild-type RT but lose potency against variants with single Y181C and double K103N/Y181C mutations. As guided by structure-based and computational studies, removal of the 5-Cl substitution of compound 1 on the catechol aryl ring system led to a new analogue compound 2 that maintains greater potency against Y181C and K103N/Y181C variants and better solubility (510 µg/mL). Crystal structures were determined for wild-type, Y181C, and K103N/Y181C RT in complex with both compounds 1 and 2 to understand the structural basis for these findings. Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket. Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket. Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.


Subject(s)
Anti-HIV Agents/chemistry , Anti-HIV Agents/pharmacology , HIV Reverse Transcriptase/antagonists & inhibitors , HIV-1/enzymology , Reverse Transcriptase Inhibitors/chemistry , Reverse Transcriptase Inhibitors/pharmacology , Cell Line , Crystallography, X-Ray , HIV Infections/drug therapy , HIV Infections/enzymology , HIV Infections/virology , HIV Reverse Transcriptase/chemistry , HIV Reverse Transcriptase/genetics , HIV-1/drug effects , HIV-1/genetics , Humans , Models, Molecular , Point Mutation , Solubility
16.
ACS Chem Biol ; 10(5): 1319-29, 2015 May 15.
Article in English | MEDLINE | ID: mdl-25686244

ABSTRACT

Human fibroblast growth factor receptors (FGFRs) 1-4 are a family of receptor tyrosine kinases that can serve as drivers of tumorigenesis. In particular, FGFR1 gene amplification has been implicated in squamous cell lung and breast cancers. Tyrosine kinase inhibitors (TKIs) targeting FGFR1, including AZD4547 and E3810 (Lucitanib), are currently in early phase clinical trials. Unfortunately, drug resistance limits the long-term success of TKIs, with mutations at the "gatekeeper" residue leading to tumor progression. Here we show the first structural and kinetic characterization of the FGFR1 gatekeeper mutation, V561M FGFR1. The V561M mutation confers a 38-fold increase in autophosphorylation achieved at least in part by a network of interacting residues forming a hydrophobic spine to stabilize the active conformation. Moreover, kinetic assays established that the V561M mutation confers significant resistance to E3810, while retaining affinity for AZD4547. Structural analyses of these TKIs with wild type (WT) and gatekeeper mutant forms of FGFR1 offer clues to developing inhibitors that maintain potency against gatekeeper mutations. We show that AZD4547 affinity is preserved by V561M FGFR1 due to a flexible linker that allows multiple inhibitor binding modes. This is the first example of a TKI binding in distinct conformations to WT and gatekeeper mutant forms of FGFR, highlighting adaptable regions in both the inhibitor and binding pocket crucial for drug design. Exploiting inhibitor flexibility to overcome drug resistance has been a successful strategy for combatting diseases such as AIDS and may be an important approach for designing inhibitors effective against kinase gatekeeper mutations.


Subject(s)
Drug Resistance, Neoplasm , Mutation , Protein Kinase Inhibitors/pharmacology , Protein-Tyrosine Kinases/antagonists & inhibitors , Receptor, Fibroblast Growth Factor, Type 1/genetics , Humans , Kinetics , Models, Molecular , Phosphorylation , Protein Conformation , Protein Kinase Inhibitors/therapeutic use , Receptor, Fibroblast Growth Factor, Type 1/chemistry
17.
Proc Natl Acad Sci U S A ; 112(3): 749-54, 2015 Jan 20.
Article in English | MEDLINE | ID: mdl-25552560

ABSTRACT

Methods to accurately predict potential drug target mutations in response to early-stage leads could drive the design of more resilient first generation drug candidates. In this study, a structure-based protein design algorithm (K* in the OSPREY suite) was used to prospectively identify single-nucleotide polymorphisms that confer resistance to an experimental inhibitor effective against dihydrofolate reductase (DHFR) from Staphylococcus aureus. Four of the top-ranked mutations in DHFR were found to be catalytically competent and resistant to the inhibitor. Selection of resistant bacteria in vitro reveals that two of the predicted mutations arise in the background of a compensatory mutation. Using enzyme kinetics, microbiology, and crystal structures of the complexes, we determined the fitness of the mutant enzymes and strains, the structural basis of resistance, and the compensatory relationship of the mutations. To our knowledge, this work illustrates the first application of protein design algorithms to prospectively predict viable resistance mutations that arise in bacteria under antibiotic pressure.


Subject(s)
Algorithms , Folic Acid Antagonists/pharmacology , Proteins/chemistry , Drug Resistance/genetics , Polymorphism, Single Nucleotide , Staphylococcus aureus/enzymology , Tetrahydrofolate Dehydrogenase/drug effects
18.
ACS Med Chem Lett ; 5(11): 1259-62, 2014 Nov 13.
Article in English | MEDLINE | ID: mdl-25408842

ABSTRACT

Catechol diethers that incorporate a 6-cyano-1-naphthyl substituent have been explored as non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). Promising compounds are reported that show midpicomolar activity against the wild-type virus and sub-20 nM activity against viral variants bearing Tyr181Cys and Lys103Asn mutations in HIV-RT. An X-ray crystal structure at 2.49 Å resolution is also reported for the key compound 6e with HIV-RT.

19.
Bioorg Med Chem Lett ; 24(17): 4158-61, 2014 Sep 01.
Article in English | MEDLINE | ID: mdl-25127103

ABSTRACT

Cryptosporidium is the causative agent of a gastrointestinal disease, cryptosporidiosis, which is often fatal in immunocompromised individuals and children. Thymidylate synthase (TS) and dihydrofolate reductase (DHFR) are essential enzymes in the folate biosynthesis pathway and are well established as drug targets in cancer, bacterial infections, and malaria. Cryptosporidium hominis has a bifunctional thymidylate synthase and dihydrofolate reductase enzyme, compared to separate enzymes in the host. We evaluated lead compound 1 from a novel series of antifolates, 2-amino-4-oxo-5-substituted pyrrolo[2,3-d]pyrimidines as an inhibitor of Cryptosporidium hominis thymidylate synthase with selectivity over the human enzyme. Complementing the enzyme inhibition compound 1 also has anti-cryptosporidial activity in cell culture. A crystal structure with compound 1 bound to the TS active site is discussed in terms of several van der Waals, hydrophobic and hydrogen bond interactions with the protein residues and the substrate analog 5-fluorodeoxyuridine monophosphate (TS), cofactor NADPH and inhibitor methotrexate (DHFR). Another crystal structure in complex with compound 1 bound in both the TS and DHFR active sites is also reported here. The crystal structures provide clues for analog design and for the design of ChTS-DHFR specific inhibitors.


Subject(s)
Cryptosporidium/enzymology , Drug Design , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Multienzyme Complexes/antagonists & inhibitors , Pyrimidines/chemistry , Pyrimidines/pharmacology , Pyrroles/chemistry , Pyrroles/pharmacology , Thymidylate Synthase/antagonists & inhibitors , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemical synthesis , Models, Molecular , Molecular Structure , Multienzyme Complexes/metabolism , Pyrimidines/chemical synthesis , Pyrroles/chemical synthesis , Structure-Activity Relationship , Tetrahydrofolate Dehydrogenase/metabolism , Thymidylate Synthase/metabolism
20.
Biochim Biophys Acta ; 1840(7): 2203-11, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24726448

ABSTRACT

BACKGROUND: Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are vital in treating HIV-1 infection by inhibiting reverse transcriptase (RT). Drug toxicity and resistance drive the need for effective new inhibitors with improved physiochemical properties and potent antiviral activity. Computer-aided and structure-based drug design have guided the addition of solubilizing substituents to the diaryltriazine scaffold. These derivatives have markedly improved solubility and maintain low nanomolar antiviral activity against RT. The molecular and structural basis of inhibition for this series was determined to facilitate future inhibitor development with improved pharmacological profiles. METHODS: The molecular mechanism of inhibition was investigated using transient-state kinetic analysis. Crystal structures of RT in complex with each inhibitor were obtained to investigate the structural basis of inhibition. RESULTS: The diaryltriazine and its morpholine derivative have RT inhibition constants of 9±2nM and 14±4nM, respectively. They adopt differential binding modes within the non-nucleoside inhibitor binding pocket to distort the catalytic site geometry and primer grip regions. The novel morpholinopropoxy substituent extends into the RT/solvent interface of the NNIBP. CONCLUSIONS: Kinetic and structural analyses show that these inhibitors behave as conventional NNRTIs and inhibit the polymerization step. This study confirms that appending solubilizing substituents on the azine ring of diaryltriazine class of NNRTIs that extend into the RT/solvent interface effectively maintains low nanomolar potency and improves physiochemical properties. GENERAL SIGNIFICANCE: The modification of NNRTI scaffolds with solubilizing substituents, which extend into the RT/solvent interface, yields potent antivirals and is an effective strategy for developing novel inhibitors with improved pharmacological properties.


Subject(s)
HIV Reverse Transcriptase/chemistry , HIV-1/enzymology , Reverse Transcriptase Inhibitors/chemistry , Triazines/chemistry , Crystallography, X-Ray , Drug Design , HIV Infections/drug therapy , HIV Infections/enzymology , HIV Infections/virology , HIV-1/drug effects , Humans , Kinetics , Mechanical Phenomena , Morpholines/chemistry , Protein Conformation , Reverse Transcriptase Inhibitors/therapeutic use , Triazines/therapeutic use
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