scholarly journals Evidence of Pyrimethamine and Cycloguanil Analogues as Dual Inhibitors of Trypanosoma brucei Pteridine Reductase and Dihydrofolate Reductase

2021 ◽  
Vol 14 (7) ◽  
pp. 636
Author(s):  
Giusy Tassone ◽  
Giacomo Landi ◽  
Pasquale Linciano ◽  
Valeria Francesconi ◽  
Michele Tonelli ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Dihydrofolate Reductase ◽  
Neglected Tropical Diseases ◽  
Binding Mode ◽  
Structural Features ◽  
Binding Modes ◽  
Substitution Pattern ◽  
Future Design ◽  
Dual Inhibitors ◽  
Etiological Agents

Trypanosoma and Leishmania parasites are the etiological agents of various threatening neglected tropical diseases (NTDs), including human African trypanosomiasis (HAT), Chagas disease, and various types of leishmaniasis. Recently, meaningful progresses in the treatment of HAT, due to Trypanosoma brucei (Tb), have been achieved by the introduction of fexinidazole and the combination therapy eflornithine–nifurtimox. Nevertheless, due to drug resistance issues and the exitance of animal reservoirs, the development of new NTD treatments is still required. For this purpose, we explored the combined targeting of two key folate enzymes, dihydrofolate reductase (DHFR) and pteridine reductase 1 (PTR1). We formerly showed that the TbDHFR inhibitor cycloguanil (CYC) also targets TbPTR1, although with reduced affinity. Here, we explored a small library of CYC analogues to understand how their substitution pattern affects the inhibition of both TbPTR1 and TbDHFR. Some novel structural features responsible for an improved, but preferential, ability of CYC analogues to target TbPTR1 were disclosed. Furthermore, we showed that the known drug pyrimethamine (PYR) effectively targets both enzymes, also unveiling its binding mode to TbPTR1. The structural comparison between PYR and CYC binding modes to TbPTR1 and TbDHFR provided key insights for the future design of dual inhibitors for HAT therapy.

High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor

2020 ◽  
Vol 76 (6) ◽  
pp. 558-564
Author(s):  
Giacomo Landi ◽  
Pasquale Linciano ◽  
Giusy Tassone ◽  
Maria Paola Costi ◽  
Stefano Mangani ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Neglected Tropical Diseases ◽  
Protozoan Parasite ◽  
Binding Mode ◽  
New Class ◽  
Hydrogen Bond Interactions ◽  
Promising Strategy ◽  
Trypanosomatid Parasites ◽  
Micromolar Range

The protozoan parasite Trypanosoma brucei is the etiological agent of human African trypanosomiasis (HAT). HAT, together with other neglected tropical diseases, causes serious health and economic issues, especially in tropical and subtropical areas. The classical antifolates targeting dihydrofolate reductase (DHFR) are ineffective towards trypanosomatid parasites owing to a metabolic bypass by the expression of pteridine reductase 1 (PTR1). The combined inhibition of PTR1 and DHFR activities in Trypanosoma parasites represents a promising strategy for the development of new effective treatments for HAT. To date, only monocyclic and bicyclic aromatic systems have been proposed as inhibitors of T. brucei PTR1 (TbPTR1); nevertheless, the size of the catalytic cavity allows the accommodation of expanded molecular cores. Here, an innovative tricyclic-based compound has been explored as a TbPTR1-targeting molecule and its potential application for the development of a new class of PTR1 inhibitors has been evaluated. 2,4-Diaminopyrimido[4,5-b]indol-6-ol (1) was designed and synthesized, and was found to be effective in blocking TbPTR1 activity, with a K i in the low-micromolar range. The binding mode of 1 was clarified through the structural characterization of its ternary complex with TbPTR1 and the cofactor NADP(H), which was determined to 1.30 Å resolution. The compound adopts a substrate-like orientation inside the cavity that maximizes the binding contributions of hydrophobic and hydrogen-bond interactions. The binding mode of 1 was compared with those of previously reported bicyclic inhibitors, providing new insights for the design of innovative tricyclic-based molecules targeting TbPTR1.

scholarly journals Cyclic peptides can engage a single binding pocket through highly divergent modes

2020 ◽  
Vol 117 (43) ◽  
pp. 26728-26738
Author(s):  
Karishma Patel ◽  
Louise J. Walport ◽  
James L. Walshe ◽  
Paul D. Solomon ◽  
Jason K. K. Low ◽  
...  
Keyword(s):  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Binding Pocket ◽  
Binding Mode ◽  
Structural Features ◽  
Binding Modes ◽  
Single Target ◽  
Bromodomain Proteins ◽  
High Degree ◽  
Drug Leads

Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.

scholarly journals Formazanate Complexes of Bis-Cyclometalated Iridium

2019 ◽  
Author(s):  
Evanta Kabir ◽  
Ge Mu ◽  
David A. Momtaz ◽  
Noah A. Bryce ◽  
Thomas Teets
Keyword(s):  
Point Group ◽  
Binding Mode ◽  
Group Symmetry ◽  
Binding Modes ◽  
X Ray Diffraction ◽  
Substitution Pattern ◽  
X Ray ◽  
Redox Active ◽  
Symmetric Geometry ◽  
New Compounds

<div>In this work we describe a series of bis-cyclometalated iridium(III) formazanate complexes, expanding the coordination chemistry of the redox-active formazanate class to iridium. A total of 18 new complexes are described, varying the substituent pattern on the formazanate and the identity of the cyclometalating ligand on iridium. Eight of the new compounds are structurally characterized by single-crystal X-ray diffraction, which along with NMR spectroscopy evinces two binding modes of the formazanate. Two of the compounds are isolated in a C2-symmetric geometry where the formazanate is bound in a six-member chelate “closed” conformation, involving the 1- and 5-positions of the 1,2,4,5-tetraazapentadienyl formazanate core. In most of the examples, the major isomer that forms and is exclusively isolated involves the formazanate bound in a five-member chelate “open” form, coordinating through the 1- and 4-positions of the formazanate core and resulting in C1 point-group symmetry. All complexes are characterized by UV-vis absorption spectroscopy and cyclic voltammetry, with these features depending primarily on the substitution pattern on the formazanate, and to a lesser extent on the identity of the cyclometalating ligand and formazanate binding mode.</div>

scholarly journals Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays

Molecules ◽  
2019 ◽  
Vol 24 (1) ◽  
pp. 142 ◽  
Author(s):  
Magambo Phillip Kimuda ◽  
Dustin Laming ◽  
Heinrich C. Hoppe ◽  
Özlem Tastan Bishop
Keyword(s):  
Trypanosoma Brucei ◽  
Dihydrofolate Reductase ◽  
Human African Trypanosomiasis ◽  
De Novo ◽  
In Vitro Testing ◽  
Binding Modes ◽  
Dual Inhibition ◽  
In Vitro Inhibition ◽  
Potential Inhibitors

Pteridine reductase 1 (PTR1) is a trypanosomatid multifunctional enzyme that provides a mechanism for escape of dihydrofolate reductase (DHFR) inhibition. This is because PTR1 can reduce pterins and folates. Trypanosomes require folates and pterins for survival and are unable to synthesize them de novo. Currently there are no anti-folate based Human African Trypanosomiasis (HAT) chemotherapeutics in use. Thus, successful dual inhibition of Trypanosoma brucei dihydrofolate reductase (TbDHFR) and Trypanosoma brucei pteridine reductase 1 (TbPTR1) has implications in the exploitation of anti-folates. We carried out molecular docking of a ligand library of 5742 compounds against TbPTR1 and identified 18 compounds showing promising binding modes. The protein-ligand complexes were subjected to molecular dynamics to characterize their molecular interactions and energetics, followed by in vitro testing. In this study, we identified five compounds which showed low micromolar Trypanosome growth inhibition in in vitro experiments that might be acting by inhibition of TbPTR1. Compounds RUBi004, RUBi007, RUBi014, and RUBi018 displayed moderate to strong antagonism (mutual reduction in potency) when used in combination with the known TbDHFR inhibitor, WR99210. This gave an indication that the compounds might inhibit both TbPTR1 and TbDHFR. RUBi016 showed an additive effect in the isobologram assay. Overall, our results provide a basis for scaffold optimization for further studies in the development of HAT anti-folates.

Formazanate Complexes of Bis-Cyclometalated Iridium

2019 ◽  
Author(s):  
Evanta Kabir ◽  
Ge Mu ◽  
David A. Momtaz ◽  
Noah A. Bryce ◽  
Thomas Teets
Keyword(s):  
Point Group ◽  
Binding Mode ◽  
Group Symmetry ◽  
Binding Modes ◽  
X Ray Diffraction ◽  
Substitution Pattern ◽  
X Ray ◽  
Redox Active ◽  
Symmetric Geometry ◽  
New Compounds

<div>In this work we describe a series of bis-cyclometalated iridium(III) formazanate complexes, expanding the coordination chemistry of the redox-active formazanate class to iridium. A total of 18 new complexes are described, varying the substituent pattern on the formazanate and the identity of the cyclometalating ligand on iridium. Eight of the new compounds are structurally characterized by single-crystal X-ray diffraction, which along with NMR spectroscopy evinces two binding modes of the formazanate. Two of the compounds are isolated in a C2-symmetric geometry where the formazanate is bound in a six-member chelate “closed” conformation, involving the 1- and 5-positions of the 1,2,4,5-tetraazapentadienyl formazanate core. In most of the examples, the major isomer that forms and is exclusively isolated involves the formazanate bound in a five-member chelate “open” form, coordinating through the 1- and 4-positions of the formazanate core and resulting in C1 point-group symmetry. All complexes are characterized by UV-vis absorption spectroscopy and cyclic voltammetry, with these features depending primarily on the substitution pattern on the formazanate, and to a lesser extent on the identity of the cyclometalating ligand and formazanate binding mode.</div>

scholarly journals The telomeric protein Pot1 from Schizosaccharomyces pombe binds ssDNA in two modes with differing 3′ end availability

2014 ◽  
Vol 42 (15) ◽  
pp. 9656-9665 ◽  
Author(s):  
Thayne H. Dickey ◽  
Deborah S. Wuttke
Keyword(s):  
Binding Mode ◽  
Structural Features ◽  
Telomere Maintenance ◽  
Binding Modes ◽  
Ssdna Binding ◽  
Telomere Protection ◽  
Ssdna Binding Protein ◽  
Length Regulation ◽  
Ob Fold ◽  
The Individual

Abstract Telomere protection and length regulation are important processes for aging, cancer and several other diseases. At the heart of these processes lies the single-stranded DNA (ssDNA)-binding protein Pot1, a component of the telomere maintenance complex shelterin, which is present in species ranging from fission yeast to humans. Pot1 contains a dual OB-fold DNA-binding domain (DBD) that fully confers its high affinity for telomeric ssDNA. Studies of S. pombe Pot1-DBD and its individual OB-fold domains revealed a complex non-additive behavior of the two OB-folds in the context of the complete Pot1 protein. This behavior includes the use of multiple distinct binding modes and an ability to form higher order complexes. Here we use NMR and biochemical techniques to investigate the structural features of the complete Pot1-DBD. These experiments reveal one binding mode characterized by only subtle alternations to the individual OB-fold subdomain structures, resulting in an inaccessible 3′ end of the ssDNA. The second binding mode, which has equivalent affinity, interacts differently with the 3′ end, rendering it available for interaction with other proteins. These findings suggest a structural switch that contributes to telomere end-protection and length regulation.

scholarly journals Identification of Novel Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and In Vitro Inhibition Assays

2018 ◽  
Author(s):  
Magambo Phillip Kimuda ◽  
Dustin Laming ◽  
Heinrich C. Hoppe ◽  
Özlem Tastan Bishop
Keyword(s):  
Trypanosoma Brucei ◽  
Dihydrofolate Reductase ◽  
Human African Trypanosomiasis ◽  
De Novo ◽  
In Vitro Testing ◽  
In Vitro Experiments ◽  
Cell Cytotoxicity ◽  
Binding Modes ◽  
Dual Inhibition

Pteridine reductase 1 is a trypanosomatid multifunctional enzyme that provides a mechanism for escape of Dihydrofolate reductase (DHFR) inhibition. This is because PTR1 can reduce pterins and folates. Trypanosomes require folates and pterins for survival and are unable to synthesize them de novo. Currently there are no anti-folate based Human African Trypanosomiasis (HAT) chemotherapeutics in use. Thus, successful dual inhibition of TbDHFR and TbPTR1 has implications in the exploitation of anti-folates. We carried out molecular docking of a ligand library of 5742 compounds against TbPTR1 and identified 18 compounds showing promising binding modes. The protein-ligand complexes were subjected to Molecular dynamics to characterize their molecular interactions and energetics followed by in vitro testing. In this study, we identified five potential TbPTR1 inhibitors that showed low micromolar Trypanosome growth inhibition in in vitro experiments with no significant human cell cytotoxicity. Compounds RUBi004, RUBi007, RUBi014, and RUBi018 displayed moderate to strong antagonism when used in combination with the known TbDHFR inhibitor, WR99210. This gave an indication that the compounds might inhibit both TbPTR1 and TbDHFR. RUBi016 showed an additive effect in the isobologram assay. Our results provide a basis for scaffold optimization for further studies in the development of HAT antifolates.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

2017 ◽  
Author(s):  
Samuel Gill ◽  
Nathan M. Lim ◽  
Patrick Grinaway ◽  
Ariën S. Rustenburg ◽  
Josh Fass ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Recent Success ◽  
Multiple Binding ◽  
Proper Sampling

<div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div>

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

2018 ◽  
Author(s):  
Samuel Gill ◽  
Nathan M. Lim ◽  
Patrick Grinaway ◽  
Ariën S. Rustenburg ◽  
Josh Fass ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Recent Success ◽  
Multiple Binding ◽  
Proper Sampling

<div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div>

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