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Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis \((\mathbf{MPDS}^{\mathbf{TB}})\)

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Abstract

Molecular Property Diagnostic Suite (\(\text {MPDS}^{\mathrm{TB}}\)) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). \(\text {MPDS}^{\mathrm{TB}}\) tool has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal, \(\text {MPDS}^{\mathrm{TB}}\) 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular.

Graphical Abstract

SYNOPSIS: A web-based \(\text {MPDS}^{\mathrm{TB}}\) Galaxy tool is developed for assessing therapeutic potential of molecules. \(\text {MPDS}^{\mathrm{TB}}\) is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular.

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Acknowledgements

We are thankful to OSDD, CSIR and Sir Dorabji TATA trust for providing TCOF fellowships to some of the authors in the study. CSIR \(12^{\mathrm{th}}\) five year program GENESIS (BSC 0121), Department of Science and Technology (New Delhi) and Department of Biotechnology (New Delhi) are also thanked for funding. Code development has taken about 5 years of time starting from 2012 and has witnessed 5 Workshops in IICT, IMTECH, OSDD centre, Bangalore, and NCL. Besides there were several exchange of students between various institutes. We thank CSIR OSDD consortium, NIPER, JNU, and BBAU for providing support. GNS thank J C Bose fellowship of DST. This manuscript is dedicated to the memory of Dr. Anirban Banerji and Dr. Pankaj Narang who have provided a lot of energy and enthusiasm during the kick-start stages of the MPDS teamwork.

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Authors and Affiliations

  1. Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India

    Anamika Singh Gaur, Lijo John, M Ram Vivek, Sridhara Janardhan, Anirban Banerji, Aparna Singh, Chinmayee Choudhury, D Arun Kumar, Karunakar Tanneeru, M Prasanthi, Nandan Kumar, N Yedukondalu, P Sri Saranya, Reetu Sharma, R Srinithi, S Hemasri & G Narahari Sastry

  2. Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India

    Anshu Bhardwaj, Arun Sharma, Rakesh Kumar, Anurag Passi, Gajendra PS Raghava, Kumardeep Chaudhary, Neeraj K Rajput & Sandeep Singh

  3. Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, 160 062, India

    Neha Tripathi, Prasad V Bharatam, Abhaysinh Mori, Harish Jangra & R Venkata Krishnan

  4. Chemical Laboratory, CSIR-Central Leather Research Institute, Chennai, 600 020, India

    Charuvaka Muvva, ER Azhagiya Singam & Subramanian Venkatesan

  5. School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India

    Andrew M Lynn, Anmol J Hemrom, Deepak R. Bharti & Pankaj Narang

  6. Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, 411 008, India

    Chinmai Madhuri, Deepak Pandit, M Karthikeyan, Vijay Khedkar & Yogesh Joshi

  7. Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, 226 025, India

    Asheesh Kumar, Devesh Kumar, Ruchi Mishra & Suresh Kumar

  8. Open Source Drug Discovery Consortium, New Delhi, India

    Hari Sailaja, Kaamini Raithatha, Prasun Dutta & Uca Jaleel

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Corresponding author

Correspondence to G Narahari Sastry.

Additional information

Deceased: ANIRBAN BANERJI and PANKAJ NARANG.

Principal investigator: G NARAHARI SASTRY

Co-principal investigators: P ANSHU BHARDWAJ, PRASAD V BHARATAM, ANDREW M LYNN, DEVESH KUMAR, GAJENDRA P S RAGHAVA, M KARTHIKEYAN, SUBRAMANIAN VENKATESAN

Core developers: ANAMIKA SINGH GAUR, ANSHU BHARDWAJ, ARUN SHARMA, LIJO JOHN, M RAM VIVEK, NEHA TRIPATHI, PRASAD V BHARATAM, RAKESH KUMAR, SRIDHARA JANARDHAN, G NARAHARI SASTRY

Co-developers: ABHAYSINH MORI, ANIRBAN BANERJI, ANMOL J HEMROM, ANURAG PASSI, APARNA SINGH, ASHEESH KUMAR, CHARUVAKA MUVVA, CHINMAI MADHURI, CHINMAYEE CHOUDHURY, D ARUN KUMAR, DEEPAK PANDIT, DEEPAK R BHARTI, ER AZHAGIYA SINGAM, HARI SAILAJA, HARISH JANGRA, KAAMINI RAITHATHA, KARUNAKAR TANNEERU, KUMARDEEP CHAUDHARY, M PRASANTHI, NANDAN KUMAR, N YEDUKONDALU, NEERAJ K RAJPUT, P SRI SARANYA, PANKAJ NARANG, PRASUN DUTTA, R VENKATA KRISHNAN, REETU SHARMA, R SRINITHI, RUCHI MISHRA, S HEMASRI, SANDEEP SINGH, SURESH KUMAR, UCA JALEEL, VIJAY KHEDKAR, YOGESH JOSHI.

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Gaur, A.S., Bhardwaj, A., Sharma, A. et al. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis \((\mathbf{MPDS}^{\mathbf{TB}})\) . J Chem Sci 129, 515–531 (2017). https://doi.org/10.1007/s12039-017-1268-4

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  • DOI: https://doi.org/10.1007/s12039-017-1268-4

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