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| '''Alpeshkumar MALDE''' <br>
| | https://atb.uq.edu.au/ |
| Automated Topology Builder (ATB) and Repository for the GROMOS family of force fields <br>
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| http://compbio.biosci.uq.edu.au/atb/ <br>
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| [[Image:Atb.png]] <br>
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| | http://orcid.org/0000-0002-8181-1619 |
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| [[Image:2hkz_crystal.png|thumb|Orientation of L-Ser in the crystal structure 2HKZ could explain selectivity over L-Thr but could not explain enantiomeric selectivity towards D-amino acids.]]
| | http://www.researcherid.com/rid/A-5341-2010 |
| [[Image:2hkz_jacs.png|thumb|Thermodynamically stable binding mode revealed by MD simulations and validated by FE calculations could explain both the selectivity as well as the mechanism of enantiomeric selectivity of family of aminoacyl-t-RNA synthetases. http://pubs.acs.org/doi/abs/10.1021/ja9002124]]
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| == Research Interests ==
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| Small molecule and biomolecular modeling: Molecular dynamics (MD) simulations, free energy (FE) and quantum mechanical (QM) calculations <br>
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| Identifying the thermodynamically stable binding modes of ligands in X-ray crystal complexes <br>
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| Force field for heteromolecular ligands and parameterization: Automated Topology Builder (ATB) and repository for GROMOS family of force fields (http://compbio.biosci.uq.edu.au/atb/) <br>
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| Computational method development in drug design: High throughput free energy calculations <br>
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| == Projects ==
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| - VALIDATION of the Automated Topology Builder (ATB) and repository for the family of GROMOS Force Field <br>
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| (http://compbio.biosci.uq.edu.au/atb/) [[Image:Atb.png|50px|]] <br>
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| - Deriving force constants for bonded terms from a HESSIAN matrix [[Image:Hessian.png|150px|]]<br>
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| - Modeling family B G-protein Coupled Receptors (B-GPCR):ligand interactions [[Image:UQ_GPCR_alpesh.png|100px]]<br>
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| - Binding of WARFARIN [[Image:Warfarin.png|150px|]] [[Image:warfarin_2.jpg|150px|]] <br>
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| - Single step high throughput FREE ENERGY calculations [[Image:SSP.png|350px|]] <br>
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| == Research Grants ==
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| “Automated Topology Builder: Force field parameterization and validation for heteromolecules“. University of Queensland Early Career Researcher (UQ-ECR), 2010, AUD 16K <br>
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| “Development of methodology for high throughput free energy calculations in drug design Applications”. Australian Research Council (ARC) Discovery Project, 2009-2011, AUD 259K. <br>
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| “Homology modeling of dihydroorotate dehydrogenase from Plasmodium falciparum for the purpose of designing selective inhibitors”, CSIR (Council of Scientific and Industrial Research, India), 2005-2007 <br>
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| == Awards and Fellowships ==
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| '''2010'''<br>
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| University of Queensland Early Career Researcher (UQ-ECR) award<br>
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| '''2009-2011'''<br>
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| ARC Australian Postdoctoral (ARC-APD) Fellowship <br>
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| '''2006'''<br>
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| IBM-Zerner Fellowship, Travel grant from CSIR, India and DST (Department of Science and Technology), India to attend Sanibel Symposium 2006 at Florida, USA <br>
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| '''2004-2006'''<br>
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| Senior Research Fellowship from CSIR, India <br>
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| '''2003-2004'''<br>
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| Project Associateship from UGC (Universities Grants Commission), India <br>
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| '''2002-2003'''<br>
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| Senior Research Fellowship from CSIR, India under NMITLI project on Bioinformatics <br>
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| '''2000-2001'''<br>
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| UGC Fellowship during M.S. (Pharm) and Gold Medal for M. S. (Pharm) <br>
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| '''1999, 2000'''<br>
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| Best Student Award during Third and Final year B. Pharm <br>
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| '''1996-2000'''<br>
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| Scholarships during all four years of B. Pharm, IPA (Indian Pharmaceutical Association) Gold Medal.
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| == Academic ==
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| '''PhD''' (Pharmaceutical Chemistry), Bombay College of Pharmacy, University of Mumbai, India 2006 <br>
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| '''MS (Pharm)''' (Medicinal Chemistry) National Institute of Pharmaceutical Education and Research (NIPER), India 2001 <br>
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| '''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2000 <br>
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| == Positions ==
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| '''2009-present''' <br>
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| ARC Australian Postdoctoral (ARC-APD) Fellow, MD group, SCMB, University of Queensland <br>
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| '''2007-2008''' <br>
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| Postdoctoral Research Fellow, MD Group, SCMB, University of Queensland <br>
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| '''2003-2006''' <br>
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| PhD Student, Bombay College of Pharmacy (University of Mumbai) <br>
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| '''2002-2003''' <br>
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| Senior Research Fellow, Dept of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India <br>
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| '''2002''' <br>
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| Chemist, Molecular Modelling and Drug Design Lab, Dr. Reddy’s Research Foundation, Hyderabad, India <br>
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| '''2000-2001'''<br>
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| M.S. Student, NIPER, India
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| == Selected Publications ==
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| Full list available at:
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| http://network.nature.com/people/U3E2C3D2E/profile | |
| *Song B, Kibler P, '''Malde A''', Kodukula K, Galande A. "Design of short linear peptides that show hydrogen bonding constraints in water." J. Am. Chem. Soc., 2010, 132, 4508-4509.
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| *'''Malde AK''' and Mark AE. "Binding and Enantiomeric Selectivity of Threonyl-tRNA Synthetase." J. Am. Chem. Soc., 2009, 131 (11), 3848-3849.
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| *Verma J, '''Malde A''', Khedkar S, Iyer P, Coutinho E. "Local Indices for Similarity Analysis (LISA)-A 3D-QSAR Formalism Based on Local Molecular Similarity". Journal of Chemical Information and Modelling, 2009, 49, 2695-2707
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| *Verma J, Khedkar V, Khedkar SA, '''Malde AK''', Prabhu A, Coutinho EC. “A Comprehensive Analysis of the Thermodynamic Events involved in Ligand-Receptor Binding using CoRIA and its variants”. Journal of Computer-Aided Molecular Design, 2008, 22, 91-104
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| *'''Malde AK''', Srivastava SS, Coutinho EC. “Understanding Interactions of Gastric Inhibitory Peptide (GIP) with its Receptor through NMR and Molecular Modelling”. Journal of Peptide Science, 2007, 13, 287-300
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| *Khedkar SA, '''Malde AK''', Coutinho EC. “Design of Inhibitors against MurF Enzyme of S. pneumoniae using Docking, 3D-QSAR and De Novo Design” Journal of Chemical Information & Modeling, 2007, 47, 1839-1846
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| *'''Malde AK''', Khedkar SA, Coutinho EC. “The B(OH)-NH Isostere is a Surrogate for the Amide bond (CO-NH) in Peptides: An Ab Initio Study”. Journal of Chemical Theory and Computation 2007, 3, 619-627
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| *Khedkar SA, '''Malde AK''', Coutinho EC “Pharmacophore Modeling in Drug Discovery and Development: An Overview”. Medicinal Chemistry, 2007, 3, 187–197
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| *Datar PA, Khedkar SA, '''Malde AK''' and Coutinho EC. “Comparative Residue Interaction Analysis (CoRIA): A 3D-QSAR Approach to Explore the Binding Contributions of Active Site Residues with Ligands”. Journal of Computer-Aided Molecular Design, 2006, 20, 343–360
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| *Nayyar A, '''Malde A''', Coutinho E, Jain R. “Three-dimensional Quantitative Structure (3D-QSAR) Activity Relationship Studies on Ring-substituted Quinoline Class of Anti-tuberculosis Agents”. Bioorganic & Medicinal Chemistry, 2006, 14, 847-856
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| *'''Malde A''', Khedkar S, Coutinho E, Saran A. "Geometry, transition states, and vibrational spectra of boron isostere of N-methylacetamide by ab initio calculations." International Journal of Quantum Chemistry, 2005, 102, 734-742
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| *Bharatam PV, Iqbal P, '''Malde A''', Tiwari R. “Electron Delocalization in Aminoguanidines”. Journal of Physical Chemistry A, 2004, 108, 10509-10517
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| *Chakraborti AK, Gopalakrishnan B, Sobhi ME, '''Malde AK'''. “3D-QSAR Studies on Thieno[3,2-d]pyrimidines as Phosphodiesterase IV Inhibitors”. Bioorganic & Medicinal Chemistry Letters, 2003, 13 (8), 1403-1408
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| == Presentations ==
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| '''Invited talks'''<br>
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| "Ligands in X-ray Crystal Complexes: A Drug Design Precautionary Tale". 61st Indian Pharmaceutical Congress 2009, 11-13 December 2009, Ahmedabad, India.
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| “Comparative Molecular Field Analysis (CoMFA): Method and Applications.” Invited talk at Workshop on Computational techniques in Drug Development at Molecular Mechanisms of Disease and Drug Action (MMDDA-2005) Conference on November 15, 2005 at Saha Institute of Nuclear Physics, Kolkata, India. <br>
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| '''Oral Presentations''' <br>
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| “Ligands in X-ray Complexes: A Drug Design Precautionary tale”. MM 2009 Molecular Modelling from Dynamical, Biomolecular and Materials Nanotechnology Perspective, 26 – 29 July 2009 at Gold Coast, Australia.
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| “The Omega Space of N-methylacetamide, N-hydroxy-N-methylacetamide and its Boron Isostere”. Oral presentation at National Symposium on Recent Trends in Molecular and Medical Biophysics (Indian Biophysics Society) organized by University of Pune during January 22 – 25, 2005 at Pune, India. <br>
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| “Solution conformation of Gastric Inhibitory Polypeptide (GIP) (1-30 amide) by NMR and MD Simulations”. National Symposium on Advances in Magnetic Resonance and its Applications & 12th National Magnetic Resonance Society (NMRS) Meeting during October 8-11, 2005 at Gulmarg, Kashmir and RRL, Jammu, India. <br>
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| '''Poster Presentations'''<br>
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| “How much can we trust the binding modes of non-standard ligands in X-ray crystal complexes?”. Gordon Research Conference – Computational Chemistry 2010, Aug 29 – Sept 3 at Les Diablerets, Switzerland. <br>
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| “High Throughput Free Energy Calculations: Application to Solvation Free Energy Estimation”. Poster presentation at World Association of Theoretical and Computational Chemists (WATOC) 2008, during September 14 – 19 at Sydney Convention and Exhibition Center, Australia. <br>
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| “The ω, φ, and ψ Preferences of Boron Peptides”. Poster presentation at 46th Sanibel Symposium organized by the Quantum Theory Project (QTP) group of University Florida, USA during 26 February – 3 March 2006 at St. Simon’s Island, Georgia, USA. <br>
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| “Three-dimensional quantitative structure (3D-QSAR) activity relationship studies on ring-substituted quinoline class of anti-tuberculosis agents”. Poster presentation at Molecular Mechanisms of Disease and Drug Action (MMDDA-2005) Conference held during November 16-18, 2005 at Saha Institute of Nuclear Physics, Kolkata, India.<br>
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| “Electron delocalization in Guanidines”. Poster presentation at 5th National Symposium in Chemistry organized by Chemical Research Society of India (CRSI) held in February 2003 at Chennai, India. <br>
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| “Computer-aided design of PDE IV inhibitors: Comparative Molecular Field Analysis (CoMFA) of some Thieno[3,2-d]pyrimidine derivatives”. Poster presentation at 54th Indian Pharmaceutical Congress (IPC) held during December 2002 at Pune, India.<br>
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| == Other Conferences ==
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| 10th International NCCR Symposium in Structural Biology, ETH Zurich, 2-3 Sept 2010, Switzerland <br>
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| National Symposium on Advances in Magnetic Resonance and its Applications & 12th National Magnetic Resonance Society (NMRS) Meeting during October 8-11, 2005 at Gulmarg, Kashmir and RRL, Jammu, India <br>
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| XXIst International Conference on Magnetic Resonance in Biological Systems (ICMRBS) organized by Nuclear Magnetic Resonance Society (NMRS) during January 16 –21, 2005 at Hyderabad, India <br>
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| National Symposium on Cellular and Molecular Biophysics (Indian Biophysics Society); organized by Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS) held during January 14-17, 2004 at Bangalore, India <br>
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| == Contact Details ==
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| ARC Australian Postdoctoral Fellow <br>
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| Molecular Dynamics Group <br>
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| School of Molecular and Microbial Sciences (SMMS) <br>
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| Molecualr Biosciences building (#76) <br>
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| The University of Queensland <br>
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| St. Lucia Campus, Brisbane, QLD 4072 <br>
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| Australia <br>
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| '''phone''': +61 7 3365 7562 <br>
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| '''Fax''': +61 7 3365 3872 <br>
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| '''email''': a.malde_at_uq.edu.au <br>
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| [[Image:[[Image:Example.jpg]][[Image:Example.jpg]]]]
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| [[Image:[[Image:Example.jpg]][[Image:Example.jpg]]]]
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