Final Report Summary - ORCHID (Open Collaborative Model for Tuberculosis Lead Optimisation) Executive Summary:--Project Context and Objectives:Tuberculosis (TB) is a disease caused by bacteria (Mycobacterium tuberculosis) affecting primarily young adults in developing countries. Although the global incidence rate is slowly falling, in 2013, an estimated 9.0 million people developed TB and 1.5 million died from the disease [1]. The present standard of care for the treatment of drug-susceptible TB is unsatisfactory, requiring 6 months of therapy with agents that can produce significant side effects. Moreover, the effectiveness of standard first-line antitubercular chemotherapy in many TB endemic areas is now further compromised by the emergence and spread of multi drug-resistant TB (MDR-TB), which requires the use of second-line drugs (SLDs) that are typically less effective, more toxic, costlier, and some require parenteral administration. Expanded use of SLDs in TB endemic areas and failures in adherence with the treatment regimens have fuelled the emergence of XDR-TB (extremely drug resistant TB) variants that are often beyond chemotherapeutic intervention. M(X)DR-TB represents a significant current threat in global public health and a potential precursor to the emergence of truly pan-resistant TB The imperative for identifying and developing new drugs effective against both drug susceptible and drug-resistant TB has therefore never been greater. Despite of the number of new TB candidates that over the last ten years have been progressed to studies in humans (clinical trials Phase-I to Phase-III) the armamentarium to fight against TB is still very limited in size and future. The main reasons for this are the extraordinary late attrition rates experimented in anti-infective drug discovery together with the complexity of the infection that requires the use of combination therapies for short treatments and to avoid the spread of resistances. New TB drugs and targets which are rapidly cidal, safe and amenable to combination with other drugs can overcome the spread of resistance to win this fight against TB. Specifically, the proposed Work Plan of ORCHID was intended to optimize the collaboration between its Public and Private Consortium partners and produce key data that could support the choice of a lead and a backup compound for further preclinical and clinical development. Collaboration at GSK Tres Cantos Development Campus in early stage Drug Discovery over the last years had resulted in the identification of a number of promising lead compounds in the fight against TB. These leads need to be further progressed and optimised into candidates for pre-clinical development through the Drug Development progression cascade. Three compound families were of particular interest: 1) InhA Inhibitors, 2) New Beta-lactam/Beta-lactamase combinations for TB and, 3) New potent whole cell anti-tubercular compounds with unknown mode of action. A preclinical package was already in place for some of them, but further work was necessary for others in order to justify the progression of a single anti-tubercular family to the more resource intensive stages of preclinical and clinical development. The project encompassed the parallel progression of the three compound families through:- Lead Optimization Chemistry efforts and MoA studies (Genetic and Proteomic) for whole cell inhibitors, - In vitro and in vivo evaluation of Beta-lactam/s alone or in combination with a Beta-lactamase inhibitor to evaluate the sterilising potential of the drug/s against TB, - Optimization of an InhA inhibitor for preclinical development. These efforts would yield candidate molecules for new "information rich" in vitro assays of anti-mycobacterial activity (intracellular activity, artificial granuloma, activity against slow/non growing bacteria and activity against clinical isolates) as well as for in vivo safety and efficacy evaluation in different animal models of infection (acute and/or chronic). At this stage a single compound family would be prioritized. Further studies were to be performed assessing the potential for shortening treatment in standalone therapy as well as in combination regimens both in vitro and in vivo. All three projects within the mini-portfolio exploit new mode of action paradigms, so no cross-resistance was expected with current drugs or leads in development. At this stage different innovative formulations with new material based on mesoporous silica for drug delivery in oral administration would be evaluated for single compounds and combinations. Finally a Preliminary Clinical Development plan would be put in place for the selected candidate molecule. In its proposal, Orchid final aim was to perform preclinical research and prepare a plan for future clinical development.[Ref 1: http://apps.who.int/iris/bitstream/10665/137094/1/9789241564809_eng.pdf?ua=1 ] Project Results:Progress in the first 3 years of the project, hence the 1st and 2nd reporting periods followed the planned activities with little or no deviation from the original description of work. All compound families progressed according to the plan. In the last period ORCHID project accelerated its pace with significant advances in two of the lines under study: beta-lactams and InhA inhibitors. ORCHID has identified an orally bioavailable TB drug candidate, faropenem, that could be brought to clinical testing, thus progressing further than originally planned. For this, an additional consortium: 'beta-lactams against TB: teaching new tricks to an old dog', in which ORCHID participated, was built and a proposal for an early bactericidal activity (EBA) study was submitted to the European & Developing Countries Clinical Trials Partnership (EDCTP), which was successfully accepted. Moving the final date to end of June 2015 was critical to perform the clinical trial and the pharmacology study on sputum samples. Moreover, the South African clinical trial sponsor of the EDCTP study, the Task Foundation, was incorporated as an additional partner of ORCHID. The trial was aimed to generate robust EBA data in tuberculosis patients with drug sensitive strains of M. tuberculosis that will be the basis for future clinical trials for beta-lactams and explore the feasibility of developing faropenem as an anti-tuberculosis oral agent. The role of ORCHID consortium was to provide the active pharmaceutical ingredient (API) and to perform clinical pharmacology on sputum samples. The trial was conducted from September 2014 to January 2015 and headline and final clinical data of Phase II EBA study will be made available to the scientific community in the coming months. Also in this period ORCHID did manage to finalise the originally planned work on InhA inhibitors. Promising results have been obtained in the past months in a study to evaluate in vivo the contribution of the thiadiazole series in combination with various anti-tubercular drugs. As a consequence, it was decided to scale up the current lead compound to complete the precandidate selection package, and in the case that the compound demonstrates a significant safety margin based on its exposure (by the end of 2015), it would be selected as a pre-clinical candidate. Overall, what ORCHID achieved in the past four and a half years is far beyond its initial objectives. Not only did the consortium complete an anti-mycobacterial phenotypic screening campaign and publically release all the information regarding the hits, but also performed a second anti-tubercular screening effort of two hundred and fifty thousand compounds recently added to the GSK collection. The compounds were further prioritized based on anti-tubercular potency and physicochemical properties. This effort has resulted in the identification of novel compounds and their hypothesized targets and the data will be released soon into the public domain, hopefully fueling future TB drug discovery and target validation programs. The ORCHID consortium created a portfolio of lead compounds for the later stages of development and moved forward three different classes of compounds: β--lactams, InhA inhibitors and whole cell inhibitors. The objective was to provide a lead and a back-up compound for further preclinical and clinical development and the consortium has already successfully participated in a clinical trial with the beta-lactams and is likely to generate two pre-candidates from the other two classes, for which a clinical development plan has already been established. The β-lactams line of research has been of great importance in the consortium. In a recent article published in Nature Medicine and entitled 'Oldie but goodie: repurposing penicillin for tuberculosis", it is described how ORCHID managed to repurpose beta-lactams and mentioned what a real paradigm shift the trial would be. And in fact it has been, because thanks to the clinical trial there is now a growing body of evidence that challenges the ineffectiveness of β-lactams for the treatment of Tuberculosis. By developing and implementing novel in vitro and in vivo research tools, the partners deciphered the mechanism of action of this class of compounds and successfully obtained the proof of concept both in vitro and in vivo. These activities have resulted in the generation of a robust package of information that was critical to support the clinical exploration of particular β -lactams as potential new drugs in the treatment of multidrug-resistant and extensively drug-resistant tuberculosis. Besides these major findings, ORCHID has also identified a new compound class that selectively kills latent stages of Mycobacterium tuberculosis. These recalcitrant bugs living within necrotic are being forced to use cholesterol as carbon source. This class of compounds inhibits the catabolic pathway of cholesterol and provoke accumulation of toxic intermediates that kill the bacteria. Combination studies in different murine models are already underway both at John Hopkins University and GSK. A preclinical candidate in this series could be the perfect complement for existing drugs and/or clinical candidates in development.Finally, a huge platform of in vitro and in vivo tools was created to enable understanding of the mode of action, the mechanism of resistance, the activity at different stages and full characterization around all of the hits discovered within ORCHID´s life.References:[2] Ballell L, Bates RH, Young RJ, Alvarez-Gomez D, Alvarez-Ruiz E, Barroso V, Blanco D, Crespo B, Escribano J, González R, Lozano S, Huss S, Santos-Villarejo A, Martín-Plaza JJ, Mendoza A, Rebollo-Lopez MJ, Remuiñan-Blanco M, Lavandera JL, Pérez-Herran E, Gamo-Benito FJ, García-Bustos JF, Barros D, Castro JP, Cammack N. Fueling open-source drug discovery: 177 small-molecule leads against tuberculosis. ChemMedChem. 2013 Feb;8(2):313-21. doi: 10.1002/cmdc.201200428. Epub 2013 Jan 10. PubMed PMID: 23307663; PubMed Central PMCID: PMC3743164. [3] Abrahams KA, Cox JA, Spivey VL, Loman NJ, Pallen MJ, Constantinidou C, Fernández R, Alemparte C, Remuiñán MJ, Barros D, Ballell L, Besra GS. Identification of novel imidazo[1,2-a]pyridine inhibitors targeting M. tuberculosis QcrB. PLoS One. 2012;7(12):e52951. doi: 10.1371/journal.pone.0052951. Epub 2012 Dec 31. PubMed PMID: 23300833; PubMed Central PMCID: PMC3534098. [4] Poce G, Bates RH, Alfonso S, Cocozza M, Porretta GC, Ballell L, Rullas J, Ortega F, De Logu A, Agus E, La Rosa V, Pasca MR, De Rossi E, Wae B, Franzblau SG, Manetti F, Botta M, Biava M. Improved BM212 MmpL3 inhibitor analogue shows efficacy in acute murine model of tuberculosis infection. PLoS One. 2013;8(2):e56980. doi: 10.1371/journal.pone.0056980. Epub 2013 Feb 21. PubMed PMID: 23437287; PubMed Central PMCID: PMC3578785. [5] Encinas L, O'Keefe H, Neu M, Remuiñán MJ, Patel AM, Guardia A, Davie CP, Pérez-Macías N, Yang H, Convery MA, Messer JA, Pérez-Herrán E, Centrella PA, Alvarez-Gómez D, Clark MA, Huss S, O'Donovan GK, Ortega-Muro F, McDowell W, Castañeda P, Arico-Muendel CC, Pajk S, Rullás J, Angulo-Barturen I, Alvarez-Ruíz E, Mendoza-Losana A, Ballell Pages L, Castro-Pichel J, Evindar G. Encoded Library Technology as a Source of Hits for the Discovery and Lead Optimization of a Potent and Selective Class of Bactericidal Direct Inhibitors of Mycobacterium tuberculosis InhA. J Med Chem. 2014 Feb 5. PubMed PMID: 24450589. [6] Kupferschmidt N, Xia X, Labrador RH, Atluri R, Ballell L, Garcia-Bennett AE. In vivo oral toxicological evaluation of mesoporous silica particles. Nanomedicine (Lond). 2013 Jan;8(1):57-64. doi: 10.2217/nnm.12.77. Epub 2012 Aug 14. PubMed PMID: 22891863. [7] Triboulet S, Dubée V, Lecoq L, Bougault C, Mainardi JL, Rice LB, Ethève-Quelquejeu M, Gutmann L, Marie A, Dubost L, Hugonnet JE, Simorre JP, Arthur M. Kinetic features of L,D-transpeptidase inactivation critical for β-lactam antibacterial activity. PLoS One. 2013 Jul 4;8(7):e67831. doi: 10.1371/journal.pone.0067831. Print 2013. PubMed PMID: 23861815; PubMed Central PMCID: PMC3701632. [8] Cordillot M, Dubée V, Triboulet S, Dubost L, Marie A, Hugonnet JE, Arthur M, Mainardi JL. In vitro cross-linking of Mycobacterium tuberculosis peptidoglycan by L,D-transpeptidases and inactivation of these enzymes by carbapenems. Antimicrob Agents Chemother. 2013 Dec;57(12):5940-5. doi: 10.1128/AAC.01663-13. Epub 2013 Sep 16. PubMed PMID: 24041897; PubMed Central PMCID: PMC3837840. [9] Soroka D, Dubée V, Soulier-Escrihuela O, Cuinet G, Hugonnet JE, Gutmann L, Mainardi JL, Arthur M. Characterization of broad-spectrum Mycobacterium abscessus class A β-lactamase. J Antimicrob Chemother. 2014 Mar;69(3):691-6. doi: 10.1093/jac/dkt410. Epub 2013 Oct 16. PubMed PMID: 24132992. [10] Keener A., Oldie but goodie: Repurposing penicillin for tuberculosis, Nature Medicine 20, 976–978, 2014. [11] Dhar N, Dubée V, Ballell L, Cuinet G, Hugonnet JE, Signorino-Gelo F, Barros D, Arthur M, McKinney JD. Rapid cytolysis of Mycobacterium tuberculosis by faropenem, an orally bioavailable beta-lactam antibiotic. Antimicrob Agents Chemother. 2015 Feb;59(2):1308-19. doi: 10.1128/AAC.03461-14. Epub 2014 Nov 24. [12] Rullas J, Dhar N, McKinney JD, García-Pérez A, Lelievre J, Diacon AH, Hugonnet JE, Arthur M, Angulo-Barturen I, Barros-Aguirre D, Ballell L. Combinations of beta-Lactam Antibiotics Currently in Clinical Trials Are Efficacious in a DHP-I-Deficient Mouse Model of Tuberculosis Infection. Antimicrob Agents Chemother. 2015 Aug;59(8):4997-9. doi: 10.1128/AAC.01063-15. Epub 2015 May 18.Potential Impact:Scientific expected outcomes: The compounds that emerge from this project, after further preclinical and/or clinical development, could eventually become components of novel regimens of drugs for the treatment of drug-sensitive TB and/or and M(X)DR-TB. They could be either a) compounds that could replace INH in the standard-of-care regimen and circumvent much of the resistance to INH found in circulating M. tuberculosis strains, b) β-lactams, one of the most effective, safe and well-understood antibacterial classes, for use in drug-sensitive or M(X)DR-TB, or c) a completely new novel anti-tubercular agent for use in combination with the current standard-of-care regimen and/or with the most promising TB regimens that are currently in development to improve and shorten treatment of drug sensitive TB and to address the emerging MDR problem.Socio-economic expected impact in the long-term: Intravenous treatments against MDR-TB have a great importance, however, the strategy in the case of beta-lactams in ORCHID was to find an orally bioavailable beta-lactam that would simplify the treatment.In this sense ORCHID was planned to develop new drugs that could be affordable for developing countries and active against drug-sensitive and drug-resistant TB, in a Public and Private collaboration setup that makes its findings open to the Scientific Community and General Public. Development of new and improved drugs and regimens should shorten and simplify TB treatment. The ultimate beneficiaries of improved, simplified and shortened TB treatments are TB-affected populations worldwide, but especially in low-income countries where about 90 percent of TB cases and TB-related deaths occur [13]. In addition to saving countless lives of those afflicted with drug-sensitive and drug-resistant TB, improved TB therapy can have a far-reaching development impact by minimizing productivity loss, decreasing the burden on health systems and freeing up valuable resources for use in other critical areas.[Ref 13- Stop TB Partnership. TB and Poverty. Stop TB Partnership Fact Sheet.]List of Websites:http://projectorchid.org/Dr. David Barros, GlaxoSmithKline I+D S.L. - Project coordinatordavid.a.barros@gsk.com
