Organometallic enzyme inhibitors
Meggers, Eric
Jerabek, Paul
Hegemann, Julian
Authmann, Andreas
Professor Meggers explains a novel approach to the synthesize of enzyme inhibitors, where his group is utilizing the unique properties of ruthenium based organometallic compounds.
 A few years ago we thought about a concept, a new concept to basically design globular defined structures by using metal scaffolds to make small molecules, small molecule inhibitors for enzyme. And you can see here in a representation here metal compounds in which the metal has just a structural role. It basically helps to basically organize the organic ligands in the active site and is basically really like a structural center and the exciting part for us about this is that of course metals can have coordination geometries that differ from the coordination geometries of carbon where you are limited to linear trigonoplana and tetrahedral coordination spheres. And I think we have shown over the last couple of years that this is really a promising approach and we designed actually compounds that have potencies that can really compete in their classes with the best organic compounds available and sometimes in some cases we think we have compounds that are better than the best organic compounds for a respective target. And I want to show you here maybe one design that we developed a few years ago in which we developed protein kinase inhibitors by using a natural product as an inspiration. You can see here on the left side the natural product star spherin which is an endodocarbazole alkyluride. You see here these two indoles and then you have a carbohydrate moiety and this compound actually binds to a protein kinase ATP binding site in an ATP competitive fashion. This heterocyclic moiety slides into the active site and can form two hydrogen bonds to the so-called hinge region of this ATP binding site and then the active site opens and this more globular carbohydrate can fill the area where the ribos moiety of ATP binds. And we basically used this as inspiration and designed compounds that have a similar shape but are simpler in their design and contain a metal compound as you can see here. You see that this what we call pyridocarbazole is quite similar to this endodocarbazole. We just basically replaced one endole for pyridine that gives us two coordination sites and we can introduce here this ruthenium fragment. You can see that this cyclopentadienyl half sandwich and the CO and this compound actually turns out to be a very potent inhibitor for this kinase GsK3 actually by a factor of 10 fold better than the natural product and over the years we actually improved the design and we ended up actually with a compound as shown here that has actually KI that is less than 5 picomolar. So this organometallic compound is actually by around 4 orders of 3 to 4 orders of magnitude more potent than this potent natural product and it's very selective for this particular protein kinase. You can even see here a coca-sid structure of this organometallic compound with this kinase GsK3 and how this compound really complements nicely the shape of this ATP binding site of this kinase GsK3. And you can actually I think you probably agree with me that this is a unique molecular structure that you probably cannot mimic with purely organic elements. You have here this ruthenium that really basically sits on the cyclopentadienyl moiety in the middle and basically builds multiple bonds to individual carbons of the CP ring. So that was actually for us a very exciting initial direction in this overall project and encourage us that really using metals as structural scaffolds is very promising and I can tell you actually these compounds are chemically very stable. You can they are not compromised in any way in a biological sample. They are stable in presence of soil. They are stable against water, oxygen. So such compounds basically are as stable as organic compounds. They just basically differ in their color instead of being white or yellow. They are maybe purple or black or sometimes blue or green. So that's the only basically difference that is obvious. But that looks like a nice system but we knew that these half-scentage compounds are somehow still limited in their structural options and we were really actually we thought it's important to move ahead and to basically expand this towards truly octahedral compounds because if you have octahedral metal center you can form six bonds. And that's kind of beautiful because do you know a carbon that can form six bonds? Do you know a carbon that can form octahedral coordination geometries? You cannot. You cannot form stable organic compounds where a carbon can make six bonds. But a lot of metal can. And if you talk about roussinium, roussinium forms very stable octahedral coordination geometries and so we want to use roussinium compounds or also in some aspect, radium and osmium compounds and rhodium compounds as basically mimics for octahedral carbon. And the reason why we think that such an octahedral coordination sphere is so promising and interesting for making small molecule inhibitors is because think about it. An octahedral center that has six monodentate ligands can actually form up to 30 sterile isomers and here you see listed all 30 sterile isomers. A carbon, an asymmetric carbon can just form two sterile isomers. So you go from four substituents to six and the number of sterile isomers increases by more than an order of magnitude from two to fifteen. And these number of sterile isomers, 30 in this case, basically is an indicator of how sophisticated such a center is to basically build globular structures because we have 30 ways to organize the six groups in the three-dimensional space. So very sophisticated structural center. If you take two of the centers, you can make 900 sterile isomers. If you have six centers, you can form in theory 27,000 sterile isomers. So the number of sterile isomers is in a certain way an indicator of complicatedness. And when you look at complicated natural product, that is actually you can basically transform this. If you have a complicated natural product and you look at the number of sterile isomers, that gives you a certain idea of how complicated the structures and how many sterile isomers you could form. And so that is basically our hypothesis for making such octahedral compounds. And that was the focus of the last years, in particular since we are in Marburg over the last two years. We really focused on moving away from these half-scentage compounds to octahedral compounds. Half-scentage was nice because they have a lower symmetry, they don't have so many sterile isomers, and it was a good starting point. But now we really want to go in complicated octahedral compounds and want to explore their potential to become inert bioactive compounds that can do really sophisticated molecular recognition. And I want to just give you one example of a recent design that I think shows very nicely how basically powerful such an approach is. We have a collaborator, Ronald Marmostan, at the Wister Institute in Philadelphia. He is very interested in this protein kinase pack one. And so what we did is we took a small library that we have in lab, a standard library of organometallic compound and screened it against this kinase and found that this compound here, NP309, was in this library the most potent compound for this kinase. This scaffold looks familiar. That is basically the GSK3 inhibitor I showed you here on this image. And so this compound NP309 turned out to be actually a quite decent inhibitor for pack one, 1000 nanomolar. So one micromolar IC50 that's considered a very nice primary hit. However, as I told you before, this scaffold very potent for GSK3. This compound in particular OH group on the indole, fluorine on the pyridine basically has an IC50 of 350 picomolar for GSK3. So you would imagine that you can never modify this scaffold and make it selective for the kinase pack one over GSK3. Seems to be mission impossible. However, anyways, we went ahead and Jassna from my group and Ronin's group, she co-crystallized this compound with pack one. And you can see here the crystal structure in particular what was exciting for us. And we saw all the hydrogen bonds that this compound basically undergoes with the active side as we expected. But however, when you look at the cut through the active side, you see that this active side is very open. And the CP ring here, shown as a space filling model, does not undergo any interaction with the active side. It just basically hangs there in a free space and can just not fill this large active side. So we thought that's actually a great model system to investigate the power of the larger octahedron compounds. And we just use this lead structure and replace the CP for this large bidented ligand and the chlorine. You can see in this space filling model that this way actually blow up the structure. And indeed we found by doing so actually this compound initially very selective for GSK3 because after this change, this compound actually is a 10-fold better for pack one. And suddenly it's basically not an inhibitor for GSK3 anymore because it does not fit into the active side. And we back this up by coagulate structure again. They're done by Yasna. And you can see all the hydrogen bonds. And what is most important, you can see here again in this cut through the active side that now this large compound can really nicely complement this open active side and fills it completely. And the distance here between the power position of the pruridin and CO, these around eight angstroms, they are like a yardstick that basically determines whether the compound can fit into an active side or not. GSK3 is not open enough. It will not fit into there. But pack one is open and it can now undergo all these interactions that are important for the affinity and selectivity. So and I think that is to our knowledge, this compound here, which we call FL411, is actually the best ATP competitive inhibitor for this protein kinase to date better than any reported purely organic compound. And it's not an organic compound. It's just a coordination compound.
 A few years ago we thought about a concept, a new concept to basically design globular  defined structures by using metal scaffolds to make small molecules, small molecule inhibitors  for enzyme.  And you can see here in a representation here metal compounds in which the metal has just  a structural role.  It basically helps to basically organize the organic ligands in the active site and is  basically really like a structural center and the exciting part for us about this is  that of course metals can have coordination geometries that differ from the coordination  geometries of carbon where you are limited to linear trigonoplana and tetrahedral coordination  spheres.  And I think we have shown over the last couple of years that this is really a promising approach  and we designed actually compounds that have potencies that can really compete in their  classes with the best organic compounds available and sometimes in some cases we think we have  compounds that are better than the best organic compounds for a respective target.  And I want to show you here maybe one design that we developed a few years ago in which  we developed protein kinase inhibitors by using a natural product as an inspiration.  You can see here on the left side the natural product star spherin which is an endodocarbazole  alkyluride.  You see here these two indoles and then you have a carbohydrate moiety and this compound  actually binds to a protein kinase ATP binding site in an ATP competitive fashion.  This heterocyclic moiety slides into the active site and can form two hydrogen bonds to the  so-called hinge region of this ATP binding site and then the active site opens and this  more globular carbohydrate can fill the area where the ribos moiety of ATP binds.  And we basically used this as inspiration and designed compounds that have a similar  shape but are simpler in their design and contain a metal compound as you can see here.  You see that this what we call pyridocarbazole is quite similar to this endodocarbazole.  We just basically replaced one endole for pyridine that gives us two coordination sites  and we can introduce here this ruthenium fragment.  You can see that this cyclopentadienyl half sandwich and the CO and this compound actually  turns out to be a very potent inhibitor for this kinase GsK3 actually by a factor of 10  fold better than the natural product and over the years we actually improved the design  and we ended up actually with a compound as shown here that has actually KI that is less  than 5 picomolar.  So this organometallic compound is actually by around 4 orders of 3 to 4 orders of magnitude  more potent than this potent natural product and it's very selective for this particular  protein kinase.  You can even see here a coca-sid structure of this organometallic compound with this  kinase GsK3 and how this compound really complements nicely the shape of this ATP binding site  of this kinase GsK3.  And you can actually I think you probably agree with me that this is a unique molecular  structure that you probably cannot mimic with purely organic elements.  You have here this ruthenium that really basically sits on the cyclopentadienyl moiety  in the middle and basically builds multiple bonds to individual carbons of the CP ring.  So that was actually for us a very exciting initial direction in this overall project  and encourage us that really using metals as structural scaffolds is very promising  and I can tell you actually these compounds are chemically very stable.  You can they are not compromised in any way in a biological sample.  They are stable in presence of soil.  They are stable against water, oxygen.  So such compounds basically are as stable as organic compounds.  They just basically differ in their color instead of being white or yellow.  They are maybe purple or black or sometimes blue or green.  So that's the only basically difference that is obvious.  But that looks like a nice system but we knew that these half-scentage compounds are somehow  still limited in their structural options and we were really actually we thought it's  important to move ahead and to basically expand this towards truly octahedral compounds  because if you have octahedral metal center you can form six bonds.  And that's kind of beautiful because do you know a carbon that can form six bonds?  Do you know a carbon that can form octahedral coordination geometries?  You cannot.  You cannot form stable organic compounds where a carbon can make six bonds.  But a lot of metal can.  And if you talk about roussinium, roussinium forms very stable octahedral coordination  geometries and so we want to use roussinium compounds or also in some aspect, radium and  osmium compounds and rhodium compounds as basically mimics for octahedral carbon.  And the reason why we think that such an octahedral coordination sphere is so promising and interesting  for making small molecule inhibitors is because think about it.  An octahedral center that has six monodentate ligands can actually form up to 30 sterile  isomers and here you see listed all 30 sterile isomers.  A carbon, an asymmetric carbon can just form two sterile isomers.  So you go from four substituents to six and the number of sterile isomers increases by  more than an order of magnitude from two to fifteen.  And these number of sterile isomers, 30 in this case, basically is an indicator of how  sophisticated such a center is to basically build globular structures because we have  30 ways to organize the six groups in the three-dimensional space.  So very sophisticated structural center.  If you take two of the centers, you can make 900 sterile isomers.  If you have six centers, you can form in theory 27,000 sterile isomers.  So the number of sterile isomers is in a certain way an indicator of complicatedness.  And when you look at complicated natural product, that is actually you can basically transform  this.  If you have a complicated natural product and you look at the number of sterile isomers,  that gives you a certain idea of how complicated the structures and how many sterile isomers  you could form.  And so that is basically our hypothesis for making such octahedral compounds.  And that was the focus of the last years, in particular since we are in Marburg over  the last two years.  We really focused on moving away from these half-scentage compounds to octahedral compounds.  Half-scentage was nice because they have a lower symmetry, they don't have so many sterile  isomers, and it was a good starting point.  But now we really want to go in complicated octahedral compounds and want to explore their  potential to become inert bioactive compounds that can do really sophisticated molecular  recognition.  And I want to just give you one example of a recent design that I think shows very nicely  how basically powerful such an approach is.  We have a collaborator, Ronald Marmostan, at the Wister Institute in Philadelphia.  He is very interested in this protein kinase pack one.  And so what we did is we took a small library that we have in lab, a standard library of  organometallic compound and screened it against this kinase and found that this compound here,  NP309, was in this library the most potent compound for this kinase.  This scaffold looks familiar.  That is basically the GSK3 inhibitor I showed you here on this image.  And so this compound NP309 turned out to be actually a quite decent inhibitor for pack  one, 1000 nanomolar.  So one micromolar IC50 that's considered a very nice primary hit.  However, as I told you before, this scaffold very potent for GSK3.  This compound in particular OH group on the indole, fluorine on the pyridine basically  has an IC50 of 350 picomolar for GSK3.  So you would imagine that you can never modify this scaffold and make it selective for the  kinase pack one over GSK3.  Seems to be mission impossible.  However, anyways, we went ahead and Jassna from my group and Ronin's group, she co-crystallized  this compound with pack one.  And you can see here the crystal structure in particular what was exciting for us.  And we saw all the hydrogen bonds that this compound basically undergoes with the active  side as we expected.  But however, when you look at the cut through the active side, you see that this active  side is very open.  And the CP ring here, shown as a space filling model, does not undergo any interaction with  the active side.  It just basically hangs there in a free space and can just not fill this large active side.  So we thought that's actually a great model system to investigate the power of the larger  octahedron compounds.  And we just use this lead structure and replace the CP for this large bidented ligand and  the chlorine.  You can see in this space filling model that this way actually blow up the structure.  And indeed we found by doing so actually this compound initially very selective for GSK3  because after this change, this compound actually is a 10-fold better for pack one.  And suddenly it's basically not an inhibitor for GSK3 anymore because it does not fit into  the active side.  And we back this up by coagulate structure again.  They're done by Yasna.  And you can see all the hydrogen bonds.  And what is most important, you can see here again in this cut through the active side  that now this large compound can really nicely complement this open active side and fills  it completely.  And the distance here between the power position of the pruridin and CO, these around eight  angstroms, they are like a yardstick that basically determines whether the compound  can fit into an active side or not.  GSK3 is not open enough.  It will not fit into there.  But pack one is open and it can now undergo all these interactions that are important  for the affinity and selectivity.  So and I think that is to our knowledge, this compound here, which we call FL411, is actually  the best ATP competitive inhibitor for this protein kinase to date better than any reported  purely organic compound.  And it's not an organic compound.  It's just a coordination compound.
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A few years ago we thought about a concept, a new concept to basically design globular defined structures by using metal scaffolds to make small molecules, small molecule inhibitors for enzyme. And you can see here in a representation here metal compounds in which the metal has just a structural role. It basically helps to basically organize the organic ligands in the active site and is basically really like a structural center and the exciting part for us about this is that of course metals can have coordination geometries that differ from the coordination geometries of carbon where you are limited to linear trigonoplana and tetrahedral coordination spheres. And I think we have shown over the last couple of years that this is really a promising approach and we designed actually compounds that have potencies that can really compete in their classes with the best organic compounds available and sometimes in some cases we think we have compounds that are better than the best organic compounds for a respective target. And I want to show you here maybe one design that we developed a few years ago in which we developed protein kinase inhibitors by using a natural product as an inspiration. You can see here on the left side the natural product star spherin which is an endodocarbazole alkyluride. You see here these two indoles and then you have a carbohydrate moiety and this compound actually binds to a protein kinase ATP binding site in an ATP competitive fashion. This heterocyclic moiety slides into the active site and can form two hydrogen bonds to the so-called hinge region of this ATP binding site and then the active site opens and this more globular carbohydrate can fill the area where the ribos moiety of ATP binds. And we basically used this as inspiration and designed compounds that have a similar shape but are simpler in their design and contain a metal compound as you can see here. You see that this what we call pyridocarbazole is quite similar to this endodocarbazole. We just basically replaced one endole for pyridine that gives us two coordination sites and we can introduce here this ruthenium fragment. You can see that this cyclopentadienyl half sandwich and the CO and this compound actually turns out to be a very potent inhibitor for this kinase GsK3 actually by a factor of 10 fold better than the natural product and over the years we actually improved the design and we ended up actually with a compound as shown here that has actually KI that is less than 5 picomolar. So this organometallic compound is actually by around 4 orders of 3 to 4 orders of magnitude more potent than this potent natural product and it's very selective for this particular protein kinase. You can even see here a coca-sid structure of this organometallic compound with this kinase GsK3 and how this compound really complements nicely the shape of this ATP binding site of this kinase GsK3. And you can actually I think you probably agree with me that this is a unique molecular structure that you probably cannot mimic with purely organic elements. You have here this ruthenium that really basically sits on the cyclopentadienyl moiety in the middle and basically builds multiple bonds to individual carbons of the CP ring. So that was actually for us a very exciting initial direction in this overall project and encourage us that really using metals as structural scaffolds is very promising and I can tell you actually these compounds are chemically very stable. You can they are not compromised in any way in a biological sample. They are stable in presence of soil. They are stable against water, oxygen. So such compounds basically are as stable as organic compounds. They just basically differ in their color instead of being white or yellow. They are maybe purple or black or sometimes blue or green. So that's the only basically difference that is obvious. But that looks like a nice system but we knew that these half-scentage compounds are somehow still limited in their structural options and we were really actually we thought it's important to move ahead and to basically expand this towards truly octahedral compounds because if you have octahedral metal center you can form six bonds. And that's kind of beautiful because do you know a carbon that can form six bonds? Do you know a carbon that can form octahedral coordination geometries? You cannot. You cannot form stable organic compounds where a carbon can make six bonds. But a lot of metal can. And if you talk about roussinium, roussinium forms very stable octahedral coordination geometries and so we want to use roussinium compounds or also in some aspect, radium and osmium compounds and rhodium compounds as basically mimics for octahedral carbon. And the reason why we think that such an octahedral coordination sphere is so promising and interesting for making small molecule inhibitors is because think about it. An octahedral center that has six monodentate ligands can actually form up to 30 sterile isomers and here you see listed all 30 sterile isomers. A carbon, an asymmetric carbon can just form two sterile isomers. So you go from four substituents to six and the number of sterile isomers increases by more than an order of magnitude from two to fifteen. And these number of sterile isomers, 30 in this case, basically is an indicator of how sophisticated such a center is to basically build globular structures because we have 30 ways to organize the six groups in the three-dimensional space. So very sophisticated structural center. If you take two of the centers, you can make 900 sterile isomers. If you have six centers, you can form in theory 27,000 sterile isomers. So the number of sterile isomers is in a certain way an indicator of complicatedness. And when you look at complicated natural product, that is actually you can basically transform this. If you have a complicated natural product and you look at the number of sterile isomers, that gives you a certain idea of how complicated the structures and how many sterile isomers you could form. And so that is basically our hypothesis for making such octahedral compounds. And that was the focus of the last years, in particular since we are in Marburg over the last two years. We really focused on moving away from these half-scentage compounds to octahedral compounds. Half-scentage was nice because they have a lower symmetry, they don't have so many sterile isomers, and it was a good starting point. But now we really want to go in complicated octahedral compounds and want to explore their potential to become inert bioactive compounds that can do really sophisticated molecular recognition. And I want to just give you one example of a recent design that I think shows very nicely how basically powerful such an approach is. We have a collaborator, Ronald Marmostan, at the Wister Institute in Philadelphia. He is very interested in this protein kinase pack one. And so what we did is we took a small library that we have in lab, a standard library of organometallic compound and screened it against this kinase and found that this compound here, NP309, was in this library the most potent compound for this kinase. This scaffold looks familiar. That is basically the GSK3 inhibitor I showed you here on this image. And so this compound NP309 turned out to be actually a quite decent inhibitor for pack one, 1000 nanomolar. So one micromolar IC50 that's considered a very nice primary hit. However, as I told you before, this scaffold very potent for GSK3. This compound in particular OH group on the indole, fluorine on the pyridine basically has an IC50 of 350 picomolar for GSK3. So you would imagine that you can never modify this scaffold and make it selective for the kinase pack one over GSK3. Seems to be mission impossible. However, anyways, we went ahead and Jassna from my group and Ronin's group, she co-crystallized this compound with pack one. And you can see here the crystal structure in particular what was exciting for us. And we saw all the hydrogen bonds that this compound basically undergoes with the active side as we expected. But however, when you look at the cut through the active side, you see that this active side is very open. And the CP ring here, shown as a space filling model, does not undergo any interaction with the active side. It just basically hangs there in a free space and can just not fill this large active side. So we thought that's actually a great model system to investigate the power of the larger octahedron compounds. And we just use this lead structure and replace the CP for this large bidented ligand and the chlorine. You can see in this space filling model that this way actually blow up the structure. And indeed we found by doing so actually this compound initially very selective for GSK3 because after this change, this compound actually is a 10-fold better for pack one. And suddenly it's basically not an inhibitor for GSK3 anymore because it does not fit into the active side. And we back this up by coagulate structure again. They're done by Yasna. And you can see all the hydrogen bonds. And what is most important, you can see here again in this cut through the active side that now this large compound can really nicely complement this open active side and fills it completely. And the distance here between the power position of the pruridin and CO, these around eight angstroms, they are like a yardstick that basically determines whether the compound can fit into an active side or not. GSK3 is not open enough. It will not fit into there. But pack one is open and it can now undergo all these interactions that are important for the affinity and selectivity. So and I think that is to our knowledge, this compound here, which we call FL411, is actually the best ATP competitive inhibitor for this protein kinase to date better than any reported purely organic compound. And it's not an organic compound. It's just a coordination compound.
molecules, small molecule inhibitors for enzyme. hydrogen bonds to the so-called hinge region of form stable organic compounds where a carbon can approach is. We have a collaborator, Ronald