title: HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.
abstract: The acquisition of drug-resistant mutations by infectious pathogens remains a pressing health concern, and the development of strategies to combat this threat is a priority. Here we have applied a general strategy, inverse design using the substrate envelope, to develop inhibitors of HIV-1 protease. Structure-based computation was used to design inhibitors predicted to stay within a consensus substrate volume in the binding site. Two rounds of design, synthesis, experimental testing, and structural analysis were carried out, resulting in a total of 51 compounds. Improvements in design methodology led to a roughly 1000-fold affinity enhancement to a wild-type protease for the best binders, from a Ki of 30-50 nM in round one to below 100 pM in round two. Crystal structures of a subset of complexes revealed a binding mode similar to each design that respected the substrate envelope in nearly all cases. All four best binders from round one exhibited broad specificity against a clinically relevant panel of drug-resistant HIV-1 protease variants, losing no more than 6-13-fold affinity relative to wild type. Testing a subset of second-round compounds against the panel of resistant variants revealed three classes of inhibitors: robust binders (maximum affinity loss of 14-16-fold), moderate binders (35-80-fold), and susceptible binders (greater than 100-fold). Although for especially high-affinity inhibitors additional factors may also be important, overall, these results suggest that designing inhibitors using the substrate envelope may be a useful strategy in the development of therapeutics with low susceptibility to resistance.
authors.affiliation: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Altman
authors.forename: Akbar
authors.initials: A
authors.lastname: Ali
authors.forename: G S Kiran Kumar
authors.initials: GS
authors.lastname: Reddy
authors.forename: Madhavi N L
authors.initials: MN
authors.lastname: Nalam
authors.forename: Saima Ghafoor
authors.initials: SG
authors.lastname: Anjum
authors.forename: Hong
authors.initials: H
authors.lastname: Cao
authors.forename: Sripriya
authors.initials: S
authors.lastname: Chellappan
authors.forename: Visvaldas
authors.initials: V
authors.lastname: Kairys
authors.forename: Miguel X
authors.initials: MX
authors.lastname: Fernandes
authors.forename: Michael K
authors.initials: MK
authors.lastname: Gilson
authors.forename: Celia A
authors.initials: CA
authors.lastname: Schiffer
authors.forename: Tariq M
authors.initials: TM
authors.lastname: Rana
authors.forename: Bruce
authors.initials: B
authors.lastname: Tidor
mesh_terms: D000465:Algorithms; D002219:Carbamates / Q000737:chemistry / Q000494:pharmacology; D018360:Crystallography, X-Ray; D000069454:Darunavir; D015195:Drug Design; D024882:Drug Resistance, Viral; D005663:Furans; D016333:HIV Protease / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D015497:HIV-1 / Q000201:enzymology*; D007700:Kinetics; D008958:Models, Molecular; D013329:Structure-Activity Relationship; D013449:Sulfonamides / Q000737:chemistry / Q000494:pharmacology
chemical_list: D002219:Carbamates; D005663:Furans; D017320:HIV Protease Inhibitors; D013449:Sulfonamides; C095108:amprenavir; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1; D000069454:Darunavir