1352598988485 7fffb663120dd173020ed4b9bc223583

Farooq Laboratory

Miami, Florida, US

My laboratory applies an array of in silico methods such as molecular modeling, molecular dynamics, virtual screening and retro screening to decipher how life works at atomic level and, in particular, to spur drug discovery for the treatment of human disease. For further info, please visit us at http://farooqlab.net.

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Molecular modeling
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We routinely model conformations of proteins alone and bound to their cognate ligands in homology with experimentally-determined structures. Additionally, we also investigate protein conformational dynamics so as to understand and identify potential regions in proteins that could lead to the rational development of novel... Show more »

We routinely model conformations of proteins alone and bound to their cognate ligands in homology with experimentally-determined structures. Additionally, we also investigate protein conformational dynamics so as to understand and identify potential regions in proteins that could lead to the rational development of novel therapeutic approaches.

In particular, we work with with geneticists to help them understand the molecular basis of disease mutations in terms of protein structure and function at atomic level. If you are interested in such protein structure-function analysis, please contact us for a quotation and/or collaborative work.

Importantly, we have also recently built an online tool to empower biologists with little or no structural biology background to be able to model protein structures alone and in complex with their ligands and much much more on their own. The only background required is some common sense and ability to work in a logical manner. This tool is available at http://structuropedia.org.

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Retro Screening
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Hard work coupled with serendipity has just landed you a new lead compound for the treatment of cancer. You are so excited and cannot wait to begin a clinical trial. You have talked about it ad nauseum to the extent that even your poor husband has begun to suffer from chronic nausea. No matter how excited you might be but you can... Show more »

Hard work coupled with serendipity has just landed you a new lead compound for the treatment of cancer. You are so excited and cannot wait to begin a clinical trial. You have talked about it ad nauseum to the extent that even your poor husband has begun to suffer from chronic nausea. No matter how excited you might be but you can never rule out the possibility that this putative magic pill may have serious side effects that rarely surface during the pre-clinical work. Do not worry about the time and dollars that may go down the drain should the clinical trial turn out to be your worst nightmare. Let us and our retro come to your rescue before you embark on this risky and expensive endeavor. "What is this retro of yours?", you might ask.

In our laboratory, we have recently developed a novel technique to determine the specificity and selectivity of putative or therapeutic drugs against their target proteins and/or macromolecules. In this procedure, dubbed retro (or reverse) screening, one proceeds in the opposite direction to the so-called virtual screening. In virtual screening, the goal is to use a protein target as a bait to identify a high-affinity ligand from a search library typically comprised of hundreds of thousands of small molecules. In contrast, retro screening employs a known drug molecule (clinically-proven, pre-clinical or a lead compound) to screen a protein library comprised of hundreds of thousands of individual structures (obtained from both experimental and modeling techniques). In other words, a known or potential drug is used as a bait to fish out proteins as potential binding partners. Accordingly, the extent to which this drug molecule cross-reacts with the human proteome provides a measure of its efficacy and the potential long-term side-effects.

Of particular note is the realization that retro screening should also hold a great deal of promise to test the protein landscape of thousands of environmental toxins, cosmetic agents and food additives whose growing influence is expected to cause havoc to human health and well-being in the twenty-first century. Given that our knowledge largely remains elusive vis-a-vis the ability of these ubiquitous chemicals to target the human proteome, retro screening should shed new light on their mechanisms of toxicity and thereby offer new insights to combat their undesirable effects.

Simply put, retro screening bears the potential to deliver medicine along four major fronts in a timely and cost-effective manner:
(1) To assess the potential side effects of pre-clinical drugs, thereby not only eliminating poor candidates for clinical trials but also saving time and money for delivering new drugs from bench to bedside.
(2) To lend structural insights into the side effects of clinical drugs, thereby empowering clinicians and patients-alike to more effectively weigh the medicinal benefits of a clinical drug.
(3) To discover novel protein targets of clinically-poven drugs, thereby allowing the use of a clinical drug for the treatment of a new disease for which there are limited alternative therapies.
(4) To shed light on the mechanisms of toxicity of ubiquitous environmental toxins, cosmetic agents and food additives, thereby allowing health care providers to not only better understand their impact on human health but also foster the development of new strategies and social trends to combat their undesirable effects.

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Virtual Drug Discovery
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Individuals in search of expertise with virtual screening of large libraries of synthetic (over 10 million) or natural-product-based (close to one million) ligands for their particular target protein need to look no further. We are the best and the finest the world over. Just contact us and we can negotiate a collaborative and/or... Show more »

Individuals in search of expertise with virtual screening of large libraries of synthetic (over 10 million) or natural-product-based (close to one million) ligands for their particular target protein need to look no further. We are the best and the finest the world over. Just contact us and we can negotiate a collaborative and/or service-based project.

In partricular, we employ structure-based rational approach to screen novel drug candidates from a virtual library comprised of close to one million natural products, nearly half of which are derived from traditional Chinese and Indian medicines. Additionally, our goal is to identify novel allosteric modulators of proteins, which bear the potential to not only lead to the development of less toxic drugs but could also be exploited to prevent rather than cure disease. For example, novel drugs that could prevent amyloid formation would serve as invaluable therapeutic tools in the treatment of neurodegenerative disorders such as Alzheimer's disease.

Natural products are small organic compounds derived from plants, microbes and marine organisms. Notably, natural products must interact with at least two proteins: one that is involved in their biosynthesis and the other being the target which they must recognize to elicit their chemical effects. Because natural products have undergone an evolutionary design and optimization over millions of years to a pristine level of molecular specificity and recognition, their superior medicinal power compared to their synthetic counterparts can be easily appreciated. For the same reason, drugs derived from natural products tend to be far less toxic with minimal side effects compared to synthetic compounds. Indeed, natural products have been used as a medicine for millenia and, even today, they constitute close to 50% of therapeutic drugs available on the market.

Importantly, the probability of finding a potential drug candidate against a target protein from natural products (~E-3) is nearly three orders of magnitude greater than the synthetic compound library (~E-6). It is noteworthy that the need for synthetic drugs only arises due to the scarcity of natural products. The chemical complexity of natural products only adds to our woes as it presents a nightmare for the medicinal chemist to reconstruct them in vitro. Nonetheless, natural products represent a glaring opportunity to discover new drugs that are more compatible with human physiology. To say that natural-product-based medicine is not only head and shoulders but also chest above synthetic drugs would be something of an understatement. What is so remarkable about natural products is that less than 1% have been hitherto tested for their biological activity. Accordingly, the vast wealth of therapeutic potential hidden in our environment must be unearthed to improve the quality of human health. Given the unprecedented availability of high-throughput technology to probe life at atomic level, it is time to bridge not mind the gap between traditional and contemporary medicine.

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Computational Modeling
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Hit Identification
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Drug Discovery & Development
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Computational & Statistical Analysis
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Drug Discovery
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